このページはRCSBの David S. Goodsell博士による「Molecule of the Month」2001年9月の記事を日本語に訳したものです。転載・引用については利用規約をご覧下さい。
「今月の分子」一覧に戻る / この記事のRCSBオリジナルサイト(英語)を見る
:翻訳 工藤高裕 (PDBj)

分子の番犬

抗体(PDB:1igt、重鎖2つ(赤・橙)、軽鎖2つ(黄)の4量体、上端左右にある窪みが基質結合部位)

抗体は我々の体内にある分子の番犬で、ウイルス、細菌などの招かれざる訪問者を監視している。抗体は血液中を循環し、触れるものは全て精細に調べている。もしそれが見慣れない外来のものであった時、抗体はその表面に強く結合する。それが、先月の「今月の分子」で紹介した 風邪ウイルスやポリオウイルス のようなウイルスであった場合、抗体が結合して包み込んでしまうことで十分感染を防げる。ところが、細菌に対しては抗体単独では対応しない。抗体が細菌の表面に結合する時は、免疫機構が持つ強力な防御機構に警告する目印としての役割を果たすのである。

対象物をつかむ

抗体および免疫機構で使われるその他の分子は特有の形をしている。それらは通常、末端に結合部位がある数個の柔軟な腕でできている。これはこう考えるとよく理解できる。抗体はこれから闘う攻撃者を前もって知ることはできないので、自由な部分を開いている、と。柔軟な腕は結合部位と一緒に動き、両腕であらゆる形の対象物をつかむ。ここに示すのは PDBエントリー 1igt から得られた抗体で、上端の左右に伸びた両腕の先それぞれ1つずつ、合計2つの結合部位を持っている。細く柔軟な鎖がこの2つの腕を下にある中心ドメインとつないでいることに注目して欲しい。抗体の中にはこれよりも長い柔軟な結合部で腕がつながれているものもあり、対象物の表面にある足がかりを探す際より広範囲に手を伸ばすことができる。また結合部位を4つまたは10個もつ抗体もあり、この抗体は各結合部位の結合力は弱いものの全体として強固に対象物と結合できる。

数の力

血液中には1億種以上の抗体がある。各種とも結合対象とする分子は異なっている。そして意外にも、全ての抗体はウイルスや細菌に出会う前に作られている。ウイルスや細菌に感染する時に特別な抗体が作られるのではない。抗体はあらかじめ作られて、ウイルスや細菌が攻撃してくるまで待っているのである。これだけたくさんの種類の抗体があれば、中には1つや2つはぴったり合って病原体に結合し、感染に対抗できるものがある。

この膨大な抗体のコレクションは、抗体を作る血球であるリンパ球の中にある遺伝子の組み換えによって作られている。各リンパ球はそれぞれ異なる型の抗体を作っていて、どんな型の抗体を作るかは抗体遺伝子がどのように組み換えられたかに依存している。抗体がウイルスや細菌に出会うと、それに応じたリンパ球が増殖し、侵入者と闘うのに必要となる特定の抗体を含んだ血液が押し寄せる。リンパ球は作り出した抗体に対して微調整も行うこともあり、これによってより強くより特異的に結合するよう仕立てられる。

抗体の構造

抗体は4つの鎖で構成されており、うち2つは長くて重い鎖(赤、橙)、あと2つは短くて軽い鎖(黄)である。特異的結合部位は2つの腕の先端、軽い鎖と重い鎖の間に作られた窪みに位置している。結合部位はタンパク質鎖に含まれる数個の環状領域で構成されており、各領域の長さと構成アミノ酸はかなり異なっている。この「非常に変化に富んだ環状領域」における違いが、抗体の種類ごとに異なる様々な型の窪みを作っていて、それぞれが別々の対象に特異的に結合する。抗体の残りの部分〜腕の残りの部分と2つの腕を結んでいる大きな定常ドメイン〜の構造は比較的一様で、抗体が他の免疫機構と相互作用する際に便利な足がかりとなる。

様々な角度からの攻撃

リゾチーム(緑)と結合した3つの抗体のFab断片(PDB:1fdl, 1YQV, 3HFM)

血液中で外来の分子が見つかると、様々な抗体がそれに結合して色々な角度から攻撃を加える。ここに示したのは3種類の異なる抗体がタンパク質リゾチーム(中央の緑色部分)に結合したものである。この結晶構造に含まれる各抗体(PDBエントリー 1fdl1yqv3hfm )はそれぞれ片方の腕(抗原結合断片(antigen-binding fragment、Fab)と呼ばれる)しか含まれない。これは研究を行いやすくするためになされた処置である。抗体の残りの部分は図の端から伸びているように示されている。各抗体は小さなリゾチーム分子に対して、全く違う場所に結合していることに注意して欲しい。

触媒のような抗体

ディールズ・アルダー反応を触媒する触媒抗体(PDB:1c1e)緑色の分子は遷移状態に似せた分子、下図はディールズ・アルダー反応

研究者は免疫機構の途方もなく種類の多い機能を賢明な方法で利用してきた。その方法とは、新たな酵素を設計するというものである。酵素は分子をゆるめて容易には進まない化学的変化を進ませることによって働く。例えば、左図下部に示したディールズ・アルダー反応(Diels-Alder reaction)を見て欲しい。左に描かれた2つの分子が一緒になって、赤で描かれた中央の不安定中間体が形成される。そして、中間体は分解され、二酸化硫黄が放出されて、右に示した目的の生成物が作られる。酵素は中間体を安定化させ、反応の開始から終了までを進みやすくしているのである。

抗体を酵素にするには、似た方法でこの中間遷移状態を安定化させる抗体を見いだす必要がある。研究者は遷移状態に似せた分子に結合する抗体(左図の緑の分子)を見いだすことでこれを成し遂げた。この抗体酵素は触媒抗体と呼ばれる。ここに示した触媒抗体は PDBエントリー 1c1e から得られたもので、左図下に示したディールズ・アルダー縮合反応を進める。これは重要なことである。なぜなら、この種の反応は天然に存在するどの他の酵素も行わないからである。他にも切断反応や縮合反応を行う抗体がPDBにたくさん登録されている。中にはそれを使う以外に反応方法がないものも含まれている。

構造をみる

抗体(PDB:1igt,1IGY,1HZH)

抗体は非常に柔軟であるため、完全な状態の抗体を研究するのは難しい。何百もあるPDBで利用可能な抗体構造のほとんどは抗体の断片である。よくあるのがFab腕に特異的結合を行う窪みが結合しただけのものである。ここに示すのは3つの完全な抗体の例である(PDBエントリー 1igt1igy1hzh )。いずれの例も構造を見るのには良い例である。どのようにして抗体がねじれて別の形に変化することができ、異なる結晶格子に詰め込まれるのかに注意して欲しい。これによって、抗体分子がその対象物に結合できる動作範囲についてある程度わかるだろう。

2001年9月時点でPDBに登録されていた抗体に関するエントリ一覧をこちらのリストに掲載しています。

抗体(Antibodies)関連PDBエントリー (2001年9月キーワード検索より)
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PDB ID Title Authors Publication Year Journal Name Volume No First Page Pubmed ID
12e8 Structure of a monoclonal 2E8 Fab antibody fragment specific for the low-density lipoprotein-receptor binding region of apolipoprotein E refined at 1.9 A. S.Trakhanov, S.Parkin, R.Raffai, R.Milne, Y.M.Newhouse, K.H.Weisgraber, B.Rupp 1999 Acta Crystallogr D
Biol Crystallogr
55 122 10089402
15c8 Ligand-Induced Conformational Changes in a Catalytic Antibody: Comparison of the Bound and Unbound Structure of Fab 5C8 K.Gruber, A.Heine, E.A.Stura, C.G.Shevlin, I.A.Wilson n/a To be Published n/a n/a n/a
1914 The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14. D.E.Birse, U.Kapp, K.Strub, S.Cusack, A.Aberg 1997 EMBO J 16 3757 9233785
1a0q A comparison of the crystallographic structures of two catalytic antibodies with esterase activity. J.L.Buchbinder, R.C.Stephenson, T.S.Scanlan, R.J.Fletterick 1998 J.Mol.Biol. 282 1033 9753552
1a14 Three-dimensional structures of single-chain Fv-neuraminidase complexes. R.L.Malby, A.J.McCoy, A.A.Kortt, P.J.Hudson, P.M.Colman 1998 J.Mol.Biol. 279 901 9642070
1nmc
1a2y A mutational analysis of binding interactions in an antigen-antibody protein-protein complex. W.Dall'Acqua, E.R.Goldman, W.Lin, C.Teng, D.Tsuchiya, H.Li, X.Ysern, B.C.Braden, Y.Li, S.J.Smith-Gill, R.A.Mariuzza 1998 Biochemistry 37 7981 9609690
1a3l An antibody exo Diels-Alderase inhibitor complex at 1.95 angstrom resolution. A.Heine, E.A.Stura, J.T.Yli-Kauhaluoma, C.Gao, Q.Deng, B.R.Beno, K.N.Houk, K.D.Janda, I.A.Wilson 1998 Science 279 1934 9506943
1a3r Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. J.Tormo, D.Blaas, N.R.Parry, D.Rowlands, D.Stuart, I.Fita 1994 EMBO J 13 2247 8194515
1a4j Immunological origins of binding and catalysis in a Diels-Alderase antibody. F.E.Romesberg, B.Spiller, P.G.Schultz, R.C.Stevens 1998 Science 279 1929 9506942
1a4k
1a57 The three-dimensional structure of a helix-less variant of intestinal fatty acid-binding protein. R.A.Steele, D.A.Emmert, J.Kao, M.E.Hodsdon, C.Frieden, D.P.Cistola 1998 Protein Sci. 7 1332 9655337
1a5f Primary and tertiary structures of the Fab fragment of a monoclonal anti-E-selectin 7A9 antibody that inhibits neutrophil attachment to endothelial cells. A.Rodriguez-Romero, O.Almog, M.Tordova, Z.Randhawa, G.L.Gilliland 1998 J.Biol.Chem 273 11770 9565600
1a6t Antibody-mediated neutralization of human rhinovirus 14 explored by means of cryoelectron microscopy and X-ray crystallography of virus-Fab complexes. Z.Che, N.H.Olson, D.Leippe, W.M.Lee, A.G.Mosser, R.R.Rueckert, T.S.Baker, T.J.Smith 1998 J Virol 72 4610 9573224
1a6u X-Ray Structures of Fv Fragment and its (4-Hydroxy-3-Nitrophenyl)Acetate Complex of Murine B1-8 Antibody T.Simon, K.Henrick, M.Hirshberg, G.Winter n/a To be Published n/a n/a n/a
1a6v
1a6w
1a7l Crystal structure of a dominant B-cell epitope from the preS2 region of hepatitis B virus in the form of an inserted peptide segment in maltodextrin-binding protein. F.A.Saul, B.V.Normand, F.Lema, G.A.Bentley 1998 J.Mol.Biol. 280 185 9654443
1a7n X-Ray Structures of D1.3 Fv Mutants C.Marks, K.Henrick, G.Winter n/a To be Published n/a n/a n/a
1a7o
1a7p
1a7q
1a7r
1aag Modeling the anti-CEA antibody combining site by homology and conformational search. M.T.Mas, K.C.Smith, D.L.Yarmush, K.Aisaka, R.M.Fine 1992 Proteins 14 483 1438186
1acy Crystal structure of the principal neutralization site of HIV-1. J.B.Ghiara, E.A.Stura, R.L.Stanfield, A.T.Profy, I.A.Wilson 1994 Science 264 82 7511253
1ad0 VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs. M.J.Banfield, D.J.King, A.Mountain, R.L.Brady 1997 Proteins 29 161 9329081
1ad9
1ae6
1clo
1adq Structure of human IgM rheumatoid factor Fab bound to its autoantigen IgG Fc reveals a novel topology of antibody-antigen interaction. A.L.Corper, M.K.Sohi, V.R.Bonagura, M.Steinitz, R.Jefferis, A.Feinstein, D.Beale, M.J.Taussig, B.J.Sutton 1997 Nat. Struct. Biol. 4 374 9145108
1ael Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange. M.E.Hodsdon, D.P.Cistola 1997 Biochemistry 36 2278 9047330
1afv Crystal structure of dimeric HIV-1 capsid protein. C.Momany, L.C.Kovari, A.J.Prongay, W.Keller, R.K.Gitti, B.M.Lee, A.E.Gorbalenya, L.Tong, J.McClure, L.S.Ehrlich, M.F.Summers, C.Carter, M.G.Rossmann 1996 Nat. Struct. Biol. 3 763 8784350
1ahw The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF.G9 complex. M.Huang, R.Syed, E.A.Stura, M.J.Stone, R.S.Stefanko, W.Ruf, T.S.Edgington, I.A.Wilson 1998 J.Mol.Biol. 275 873 9480775
1fgn
1tfh
1ai1 Structure-based design of a constrained peptide mimic of the HIV-1 V3 loop neutralization site. J.B.Ghiara, D.C.Ferguson, A.C.Satterthwait, H.J.Dyson, I.A.Wilson 1997 J.Mol.Biol. 266 31 9054968
1aif Structure of an anti-idiotypic Fab against feline peritonitis virus-neutralizing antibody and a comparison with the complexed Fab. N.Ban, C.Escobar, K.W.Hasel, J.Day, A.Greenwood, A.McPherson 1995 FASEB J 9 107 7821749
1aj7 Structural insights into the evolution of an antibody combining site. G.J.Wedemayer, P.A.Patten, L.H.Wang, P.G.Schultz, R.C.Stevens 1997 Science 276 1665 9180069
2rcs
1ap2 A single chain Fv fragment of P-glycoprotein-specific monoclonal antibody C219. Design, expression, and crystal structure at 2.4 A resolution. F.J.Hoedemaeker, T.Signorelli, K.Johns, D.A.Kuntz, D.R.Rose 1997 J.Biol.Chem 272 29784 9368049
1aqk Three-dimensional structure of a human Fab with high affinity for tetanus toxoid. C.Faber, L.Shan, Z.Fan, L.W.Guddat, C.Furebring, M.Ohlin, C.A.Borrebaeck, A.B.Edmundson 1998 Immunotechnology 3 253 9530559
1ar1 Structure at 2.7 A resolution of the Paracoccus denitrificans two- subunit cytochrome c oxidase complexed with an antibody FV fragment. C.Ostermeier, A.Harrenga, U.Ermler, H.Michel 1997 Proc. Natl. Acad.
Sci. USA
94 10547 9380672
1atm Three-dimensional model of the BR96 monoclonal antibody variable fragment. J.Bajorath 1994 Bioconjug Chem 5 213 7522581
1axs The interplay between binding energy and catalysis in the evolution of a catalytic antibody. H.D.Ulrich, E.Mundorff, B.D.Santarsiero, E.M.Driggers, R.C.Stevens, P.G.Schultz 1997 Nature 389 271 9305839
1axt Immune versus natural selection: antibody aldolases with enzymic rates but broader scope. .3.Barbas 3rd, A.Heine, G.Zhong, T.Hoffmann, S.Gramatikova, R.Bjornestedt, B.List, J.Anderson, E.A.Stura, I.A.Wilson, R.A.Lerner 1997 Science 278 2085 9405338
1ay1 Structural studies on an inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition. R.Murali, M.Helmer-Citterich, D.J.Sharkey, E.R.Scalice, J.L.Daiss, M.A.Sullivan, H.M.Krishna Murthy 1998 Protein Eng 11 79 9605541
1b03 A cis proline turn linking two beta-hairpin strands in the solution structure of an antibody-bound HIV-1IIIB V3 peptide. V.Tugarinov, A.Zvi, R.Levy, J.Anglister 1999 Nat. Struct. Biol. 6 331 10201400
1b2w Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an anti-gamma-interferon antibody. Z.c.Fan, L.Shan, B.Z.Goldsteen, L.W.Guddat, A.Thakur, N.F.Landolfi, M.S.Co, M.Vasquez, C.Queen, P.A.Ramsland, A.B.Edmundson 1999 J Mol Recognit 12 19 10398393
1b4j
1baf 2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten. A.T.Brunger, D.J.Leahy, T.R.Hynes, R.O.Fox 1991 J.Mol.Biol. 221 239 1920408
1bbd Three-dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2. J.Tormo, E.Stadler, T.Skern, H.Auer, O.Kanzler, C.Betzel, D.Blaas, I.Fita 1992 Protein Sci. 1 1154 1338980
1bbj Crystal structure of a chimeric Fab' fragment of an antibody binding tumour cells. R.L.Brady, D.J.Edwards, R.E.Hubbard, J.S.Jiang, G.Lange, S.M.Roberts, R.J.Todd, J.R.Adair, J.S.Emtage, D.J.King, et al. 1992 J.Mol.Biol. 227 253 1522589
1bev Implications for viral uncoating from the structure of bovine enterovirus. M.Smyth, J.Tate, E.Hoey, C.Lyons, S.Martin, D.Stuart 1995 Nat. Struct. Biol. 2 224 7773791
1bey Crystal structures of a rat anti-CD52 (CAMPATH-1) therapeutic antibody Fab fragment and its humanized counterpart. G.M.Cheetham, G.Hale, H.Waldmann, A.C.Bloomer 1998 J.Mol.Biol. 284 85 9811544
1bfo
1bfv Antibody fragment Fv4155 bound to two closely related steroid hormones: the structural basis of fine specificity. C.H.Trinh, S.D.Hemmington, M.E.Verhoeyen, S.E.Phillips 1997 Structure 5 937 9261086
1cfv
2bfv
1bgx Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme. R.Murali, D.J.Sharkey, J.L.Daiss, H.M.Murthy 1998 Proc. Natl. Acad.
Sci. USA
95 12562 9770525
1bhg Structure of human beta-glucuronidase reveals candidate lysosomal targeting and active-site motifs. S.Jain, W.B.Drendel, Z.W.Chen, F.S.Mathews, W.S.Sly, J.H.Grubb 1996 Nat. Struct. Biol. 3 375 8599764
1bj1 VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface. Y.A.Muller, Y.Chen, H.W.Christinger, B.Li, B.C.Cunningham, H.B.Lowman, A.M.de Vos 1998 Structure 6 1153 9753694
1bjm Three quaternary structures for a single protein. D.B.Huang, C.F.Ainsworth, F.J.Stevens, M.Schiffer 1996 Proc. Natl. Acad.
Sci. USA
93 7017 8692936
3bjl
4bjl
1bln Mode of binding of anti-P-glycoprotein antibody MRK-16 to its antigen. A crystallographic and molecular modeling study. S.Vasudevan, T.Tsuruo, D.R.Rose 1998 J.Biol.Chem 273 25413 9738009
1bm3 Conformational change in an anti-integrin antibody: structure of OPG2 Fab bound to a beta 3 peptide. R.Kodandapani, L.Veerapandian, C.Z.Ni, C.K.Chiou, R.M.Whittal, T.J.Kunicki, K.R.Ely 1998 Biochem Biophys
Res Commun
251 61 9790907
1bog Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity. T.Keitel, A.Kramer, H.Wessner, C.Scholz, J.Schneider-Mergener, W.Hohne 1997 Cell 91 811 9413990
1cfn
1cfq
1cfs
1cft
1boy Crystal structure of the extracellular region of human tissue factor. K.Harlos, D.M.Martin, D.P.O'Brien, E.Y.Jones, D.I.Stuart, I.Polikarpov, A.Miller, E.G.Tuddenham, C.W.Boys 1994 Nature 370 662 8065454
1bql Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment. S.Chacko, E.W.Silverton, S.J.Smith-Gill, D.R.Davies, K.A.Shick, K.A.Xavier, R.C.Willson, P.D.Jeffrey, C.Y.Chang, L.C.Sieker, S.Sheriff 1996 Proteins 26 55 8880929
1bvk Conformational correction mechanisms aiding antigen recognition by a humanized antibody. M.A.Holmes, T.N.Buss, J.Foote 1998 J Exp Med 187 479 9463398
1bvl Structural consequences of humanizing an antibody. M.A.Holmes, J.Foote 1997 J Immunol 158 2192 9036965
1bwy Three-dimensional structure of bovine heart fatty-acid-binding protein with bound palmitic acid, determined by multidimensional NMR spectroscopy. D.Lassen, C.Lucke, M.Kveder, A.Mesgarzadeh, J.M.Schmidt, B.Specht, A.Lezius, F.Spener, H.Ruterjans 1995 Eur J Biochem 230 266 7601110
1bz7 The Role of Homophilic Binding in Anti-Tumor Antibody R24 Recognition of Molecular Surfaces. Demonstration of an Intermolecular Beta-Sheet Interaction between Vh Domains M.J.Kaminski, C.R.Mackenzie, M.J.Mooibroek, T.E.S.Dahms, T.Hirama, A.N.Houghton, P.B.Chapman, S.V.Evans 1999 J.Biol.Chem. 274 5597 10026176
1r24
1bzq A Single-Domain Antibody Fragment in Complex with Rnase A: Non-Canonical Loop Structures and Nanomolar Affinity Using Two Cdr Loops. K.Decanniere, A.Desmyter, M.Lauwereys, M.Ghahroudi, S.Muyldermans, L.Wyns 1999 Structure
(London)
7 361 10196124
1c08 Crystal Structure of Anti-Hen Egg White Lysozyme Antibody (Hyhel-10) Fv- Antigen Complex. Local Structural Changes in the Protein Antigen and Water- Mediated Interactions of Fv-Antigen and Light Chain-Heavy Chain Interfaces. H.Kondo, M.Shiroishi, M.Matsushima, K.Tsumoto, I.Kumagai 1999 J.Biol.Chem. 274 27623 10488102
1c12 Insight in Odorant Perception: The Crystal Structure and Binding Characteristics of Antibody Fragments Directed Against the Musk Odorant Traseolide A.C.Langedijk, S.Spinelli, C.Anguille, P.Hermans, J.Nederlof, J.Butenandt, A.Honegger, C.Cambillau, A.Pluckthun 1999 J.Mol.Biol. 292 855 10525411
1c1e Evolution of Shape Complementarity and Catalytic Efficiency from a Primordial Antibody Template J.Xu, Q.Deng, J.Chen, K.N.Houk, J.Bartek, D.Hilvert, I.A.Wilson 1999 Science 286 2345 10600746
1c5b Catalysis of Decarboxylation by a Preorganized Heterogeneous Microenvironment: Crystal Structures of Abzyme 21D8 K.Hotta, D.Tantillo, H.Lange, K.N.Houk, D.Hilvert, I.A.Wilson 2000 J.Mol.Biol. 302 1213 11183784
1c5c
1c5d The Crystal Structure of the Fab Fragment of a Rat Monoclonal Antibody Against the Main Immunogenic Region of the Human Muscle Acetylcholine Receptor M.Kontou, D.D.Leonidas, E.H.Vatzaki, P.Tsantili, A.Mamalaki, N.G.Oikonomakos, K.R.Acharya, S.J.Tzartos 2000 Eur.J.Biochem. 267 2389 10759865
1j5o Lamivudine (3Tc) Resistance in HIV-1 Reverse Transcriptase Involves Steric Hindrance with Beta-Branched Aminoacids S.G.Sarafianos, K.Das, A.D.Clark Jr., J.Ding, P.L.Boyer, S.H.Hughes, E.Arnold 1999 Proc. Natl. Acad.
Sci. USA
96 10027 10468556
1cbv An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex. J.N.Herron, X.M.He, D.W.Ballard, P.R.Blier, P.E.Pace, A.L.Bothwell, E.W.Voss Jr., A.B.Edmundson 1991 Proteins Struct.
Funct. Genet.
11 159 1749770
1nbv
1ce1 1.9A Structure of the Therapeutic Antibody Campath-1H Fab in Complex with a Synthetic Peptide Ligand L.C.James, G.Hale, H.Waldmann, A.C.Bloomer 1999 J.Mol.Biol. 289 293 10366506
1cf8 Convergence of Catalytic Antibody and Terpene Cyclase Mechanisms: Polyene Cyclization Directed by Carbocation-Pi Interactions C.M.Paschall, J.Hasserodt, T.Jones, R.A.Lerner, K.D.Janda, D.W.Christianson 1999 Angew. Chem.
Intern. Edition
38 1743 n/a
1cgs Local and transmitted conformational changes on complexation of an anti-sweetener Fab. L.W.Guddat, L.Shan, J.M.Anchin, D.S.Linthicum, A.B.Edmundson 1994 J.Mol.Biol. 236 247 7893280
2cgr
1cic Three-dimensional structure of an idiotope-anti-idiotope complex. G.A.Bentley, G.Boulot, M.M.Riottot, R.J.Poljak 1990 Nature 348 254 1700305
1cl7 Inhibition of the HIV-1 and HIV-2 Proteases by a Monoclonal Antibody J.Lescar, J.Brynda, P.Rezacova, R.Stouracova, M.-M.Riottot, V.Chitarra, M.Fabry, M.Horejsi, J.Sedlacek, G.A.Bentley 1999 Protein Sci. 8 2686 10631984
1cly The x-ray structure of an anti-tumour antibody in complex with antigen. P.D.Jeffrey, J.Bajorath, C.Y.Chang, D.Yelton, I.Hellstrom, K.E.Hellstrom, S.Sheriff 1995 Nat. Struct. Biol. 2 466 7664109
1clz
1cqk Folding and association of the antibody domain CH3: prolyl isomerization preceeds dimerization. M.J.W.Thies, J.Mayer, J.Augustine, C.Frederick, H.Lilie, J.Buchner 1999 J.Mol.Biol. 293 67 10512716
1cr9 Antibody Binding Defines a Structure for an Epitope that Participates in the Prpc-->Prpsc Conformational Change Z.F.Kanyo, K.M.Pan, R.A.Williamson, D.R.Burton, S.B.Prusiner, R.J.Fletterick, F.E.Cohen 1999 J.Mol.Biol. 293 855 10543972
1cu4
1cs9 Structure of Antibody-Bound Peptides and Retro-Inverso Analogues. A Transferred Nuclear Overhauser Effect Spectroscopy and Molecular Dynamics Approach A.Phan Chan Du, M.C.Petit, G.Guichard, J.P.Briand, S.Muller, M.T.Cung 2001 Biochemistry 40 5720 11341837
1ct6
1cvq
1cw8
1cwz
1csy Solution structure of the C-terminal SH2 domain of the human tyrosine kinase Syk complexed with a phosphotyrosine pentapeptide. S.S.Narula, R.W.Yuan, S.E.Adams, O.M.Green, J.Green, T.B.Philips, L.D.Zydowsky, M.C.Botfield, M.Hatada, E.R.Laird, et al. 1995 Structure 3 1061 8590001
1csz
1ct8 Diverse Structural Solutions to Catalysis in a Family of Antibodies B.Gigant, T.Tsumuraya, I.Fujii, M.Knossow 1999 Structure
(London)
7 1385 10574796
1cz8 Selection and Analysis of an Optimized Anti-Vegf Antibody: Crystal Structure of an Affinity-Matured Fab in Complex with Antigen Y.Chen, C.Wiesmann, G.Fuh, B.Li, H.W.Christinger, P.Mckay, A.M.De Vos, H.B.Lowman 1999 J.Mol.Biol. 293 865 10543973
1d5b Conformational Effects in Biological Catalysis: An Antibody-Catalyzed Oxy-Cope Rearrangement E.C.Mundorff, M.A.Hanson, A.Varvak, H.Ulrich, P.G.Schultz, R.C.Stevens 2000 Biochemistry 39 627 10651626
1d5i
1d6v
1dba Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex. J.H.Arevalo, E.A.Stura, M.J.Taussig, I.A.Wilson 1993 J.Mol.Biol. 231 103 8496956
1dbb
1dbj Molecular basis of crossreactivity and the limits of antibody-antigen complementarity. J.H.Arevalo, M.J.Taussig, I.A.Wilson 1993 Nature 365 859 8413674
1dbk
1dbm
2dbl
1dc9 Properties and Crystal Structure of a Beta-Barrel Folding Mutant I.J.Ropson, B.C.Yowler, P.M.Dalessio, L.Banaszak, J.Thompson 2000 Biophys.J. 78 1551 10692339
1dcl Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms. K.R.Ely, J.N.Herron, M.Harker, A.B.Edmundson 1989 J.Mol.Biol. 210 601 2515285
2mcg
3mcg
1dee Crystal Structure of a Staphylococcus Aureus Protein a Domain Complexed with the Fab Fragment of a Human Igm Antibody: Structural Basis for Recognition of B-Cell Receptors and Superantigen Activity M.Graille, E.A.Stura, A.L.Corper, B.J.Sutton, M.J.Taussig, J.B.Charbonnier, G.J.Silverman 2000 Proc. Natl. Acad.
Sci. USA
97 5399 10805799
1dfb Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1. X.M.He, F.Ruker, E.Casale, D.C.Carter 1992 Proc. Natl. Acad.
Sci. USA
89 7154 1496010
1dgx Fully Synthetic Human Combinatorial Antibody Libraries (Hucal) Based on Modular Consensus Frameworks and Cdrs Randomized with Trinucleotides A.Knappik, L.Ge, A.Honegger, P.Pack, M.Fischer, G.Wellnhofer, A.Hoess, J.Woelle, A.Plueckthun, B.Virnekaes 2000 J.Mol.Biol. 296 57 10656818
1dh4
1dh5
1dh6
1dh7
1dh8
1dh9
1dha
1dho
1dhq
1dhu
1dhv
1dhw
1dhz
1dl7 The Structural Basis of Repertoire Shift in an Immune Response to Phosphocholine M.Brown, M.A.Schumacher, G.D.Wiens, R.G.Brennan, M.B.Rittenberg 2000 J.Exp.Med. 191 2101 10859335
1dlf The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody. M.Nakasako, H.Takahashi, I.Shimada, Y.Arata 1999 J.Mol.Biol. 291 117 10438610
2dlf
1dn0 Three-Dimensional Structure of the Fab from a Human Igm Cold Agglutinin A.Cauerhff, B.Braden, J.G.Carvalho, R.Aparicio, I.Polikarpov, J.Leoni, F.Goldbaum 2000 J.Immunol. 165 6422 11086081
1dqd Structure of Fab Hgr-2 F6, a Competitive Antagonist of the Glucagon Receptor L.M.Wright, A.M.Brzozowski, R.E.Hubbard, A.C.W.Pike, S.M.Roberts, R.N.Skovgaard, I.Svendsen, H.Vissing, R.P.Bywater 2000 Acta Crystallogr.,
Sect.D
56 573 10771426
1dqj Three-Dimensional Structure of the Free and Antigen-Bound Fab from Monoclonal Antilysozyme Antibody Hyhel-63 Y.Li, H.Li, S.J.Smith-Gill, R.A.Mariuzza 2000 Biochemistry 39 6296 10828942
1dql An Unusual Human Igm Antibody with a Protruding Hcdr3 and High Avidity for its Peptide Ligands P.A.Ramsland, L.Shan, C.R.Moomaw, C.A.Slaughter, Z.Fan, L.W.Guddat, A.B.Edmundson 2000 Mol.Immunol. 37 295 11000403
1dqm Three-Dimensional Structures of the Free and Antigen-Bound Fab from Monoclonal Antilysozyme Antibody Hyhel-63 Y.Li, H.Li, S.J.Smith-Gill, R.A.Mariuzza 2000 Biochemistry 39 6296 10828942
1dqq
1dsf Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: conformational influence of an engineered disulfide bond. O.Almog, I.Benhar, G.Vasmatzis, M.Tordova, B.Lee, I.Pastan, G.L.Gilliland 1998 Proteins 31 128 9593187
1dvf Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 A resolution. B.C.Braden, B.A.Fields, X.Ysern, W.Dall'Acqua, F.A.Goldbaum, R.J.Poljak, R.A.Mariuzza 1996 J.Mol.Biol. 264 137 8950273
1dx2 Guided Selection of a Pan Carcinoma Specific Antibody Reveals Similar Binding Characteristics Yet Structural Divergence between the Original Murine Antibody and its Human Equivalent. S.H.W.Beiboer, A.Reurs, R.C.Roovers, J.-W.Arends, N.R.J.Whitelegg, A.R.Rees, H.R.Hoogenboom 2000 J.Mol.Biol. 296 833 10677285
1dx3
1dxz Spatial Structure of the M2 Transmembrane Segment of the Nicotinic Acetylcholine Receptor Alpha-Subunit V.S.Pashkov, I.V.Maslennikov, L.D.Tchikin, R.G.Efremov, V.T.Ivanov, A.S.Arseniev 1999 FEBS Lett. 457 117 10486576
1dzb Crystal Structure of a Phage Library-Derived Single-Chain Fv Fragment Complexed with Turkey Egg-White Lysozyme at 2.0 A Resolution J.Ay, T.Keitel, G.Kuttner, H.Wessner, C.Scholz, M.Hahn, W.Hohne 2000 J.Mol.Biol. 301 239 10926506
1e07 Structural Models for Carcinoembryonic Antigen and its Complex with the Single-Chain Fv Antibody Molecule Mfe23 M.K.Boehm, S.J.Perkins 2000 FEBS Lett. 475 11 10854848
1e4k The 3.2A Crystal Structure of the Human Igg1 Fc Fragment-Fc-Gamma-Riii Complex P.Sondermann, R.Huber, V.Oosthuizen, U.Jacob 2000 Nature 406 267 10917521
1e4w Cross-reactive binding of cyclic peptides to an anti-TGFalpha antibody Fab fragment: an X-ray structural and thermodynamic analysis. M.Hahn, D.Winkler, K.Wlefle, R.Misselwitz, H.Wlefle H.Wessner, G.Zahn, C. Scholz, M. Seifert, R. Harkins, J.Schneider-Mergener, W.Hohne 2001 J.Mol.Biol. 314 293 11718562
1e4x
1e6j Mutual Conformational Adaptations in Antigen and Antibody Upon Complex Formation between an Fab and HIV-1 Capsid Protein P24 S.Monaco-Malbet, C.Berthet-Colominas, A.Novelli, N.Battai, N.Piga, V.Cheynet, F.Mallet, S.Cusack 2000 Structure Fold.
Des.
8 1069 11080628
1e6o
1e8l A Refined Solution Structure of Hen Lysozyme Determined Using Residual Dipolar Coupling Data H.Schwalbe, S.B.Grimshaw, A.Spencer, M.Buck, J.Boyd, C.M.Dobson, C.Redfield, L.J.Smith 2001 Protein Sci. 10 677 11274458
1eap Crystal structure of a catalytic antibody with a serine protease active site. G.W.Zhou, J.Guo, W.Huang, R.J.Fletterick, T.S.Scanlan 1994 Science 265 1059 8066444
1egj Structure of the Activation Domain of the Gm-Csf/Il-3/Il-5 Receptor Common Beta-Chain Bound to an Antagonist J.Rossjohn, W.J.Mckinstry, J.M.Woodcock, B.J.Mcclure, T.R.Hercus, M.W.Parker, A.F.Lopez, C.J.Bagley 2000 Blood 95 2491 10753826
1ehl Crystal Structure of the 64M-2 Antibody Fab Fragment in Complex with a DNA Dt(6-4)T Photoproduct Formed by Ultraviolet Radiation H.Yokoyama, R.Mizutani, Y.Satow, Y.Komatsu, E.Ohtsuka, O.Nikaido 2000 J.Mol.Biol. 299 711 10835279
1ejo A Multiply Substituted G-H Loop from Foot-and-Mouth Disease Virus in Complex with a Neutralizing Antibody: A Role for Water Molecules W.F.Ochoa, S.G.Kalko, M.G.Mateu, P.Gomes, D.Andreu, E.Domingo, I.Fita, N.Verdaguer 2000 J.Gen.Virol. 81 1495 10811933
1em4 Stabilization of bound polycyclic aromatic hydrocarbons by a pi-cation interaction. J.-L.Pellequer, B.Zhao, H.-I.Kao, C.W.Bell, K.Li, Q.X.Li, A.E.Karu, V.A.Roberts 2000 J.Mol.Biol. 302 691 10986127
1emt X-Ray Crystal Structure of an Anti-Buckminsterfullerene Antibody Fab Fragment: Biomolecular Recognition of C60 B.C.Braden, F.A.Goldbaum, B.-X.Chen, A.N.Kirschner, S.R.Wilson, B.F.Erlanger 2000 Proc. Natl. Acad.
Sci. USA
97 12193 11035793
1eo8 Structural Evidence for Recognition of a Single Epitope by Two Distinct Antibodies D.Fleury, R.S.Daniels, J.J.Skehel, M.Knossow, T.Bizebard 2000 Proteins: Struct.,
Funct., Genet.
40 572 10899782
1etz The Three-Dimensional Structure of a Complex of a Murine Fab (Nc10.14) With a Potent Sweetener (Nc174): An Illustration of Structural Diversity in Antigen Recognition by Immunoglobulins L.W.Guddat, L.Shan, C.Broomell, P.A.Ramsland, Z.Fan, J.M.Anchin, D.S.Linthicum, A.B.Edmundson 2000 J.Mol.Biol. 302 853 10993728
1ezv Structure at 2.3 A Resolution of the Cytochrome Bc1 Complex from the Yeast Saccharomyces Cerevisiae Co-Crystallized with an Antibody Fv Fragment C.Hunte, J.Koepke, C.Lange, T.Rossmanith, H.Michel 2000 Structure 8 669 10873857
1f11 Structure of the Fab Fragment from F124, a Monoclonal Antibody Specific for Hepatitis B Surface Antigen F.A.Saul, B.Vulliez-Le Normand, M.Passafiume, M.M.Riottot, G.A.Bentley 2000 Acta Crystallogr.,
Sect.D
56 945 10944330
1f2x Canonical Antigen-Binding Loop Structures in Immunoglobulins: More Structures, More Canonical Classes? K.Decanniere, S.Muyldermans, L.Wyns 2000 J.Mol.Biol. 300 83 10864500
1f3d Structural Evidence for a Programmed General Base in the Active Site of a Catalytic Antibody. B.Golinelli-Pimpaneau, O.Goncalves, T.Dintinger, D.Blanchard, M.Knossow, C.Tellier 2000 Proc. Natl. Acad.
Sci. USA
97 9892 10963661
1f3r The Third-Dimensional Structure of the Complex between an Fv Antibody Fragment and an Analogue of the Main Immunogenic Region of the Acetylcholine Receptor: A Combined Two-Dimensional NMR, Homology, and Molecular Modeling Approach J.Kleinjung, M.-C.Petit, P.Orlewski, A.Mamalaki, S.-J.Tzartos, V.Tsikaris, M.Sakarellos-Daitsiotis, C.Sakarellos, M.Marraud, M.-T.Cung 2000 Biopolymers 53 113 10679615
1f4w Crystal Structure of an Anti-Carbohydrate Antibody Directed Against Vibrio Cholerae O1 in Complex with Antigen: Molecular Basis for Serotype Specificity S.Villeneuve, H.Souchon, M.M.Riottot, J.C.Mazie, P.S.Lei, C.P.J.Glaudemans, P.Kovac, J.M.Fournier, P.M.Alzari 2000 Proc. Natl. Acad.
Sci. USA
97 8433 10880560
1f4x
1f4y
1f58 Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs. R.Stanfield, E.Cabezas, A.Satterthwait, E.Stura, A.Profy, I.Wilson 1999 Structure Fold Des 7 131 10368281
2f58
3f58
1f6a Structure of the Fc Fragment of Human Ige Bound to its High-Affinity Receptor Fc(Epsilon)Ri(Alpha) S.C.Garman, B.A.Wurzburg, S.S.Tarchevskaya, J.P.Kinet, T.S.Jardetzky 2000 Nature 406 259 10917520
1f8t Spatial structure of a Fab-fragment of a monoclonal antibody to human interleukin-2 in two crystalline forms at a resolution of 2.2 and 2.9 angstroms A.V.Fokin, P.V.Afonin, I.I.Mikhailova, I.N.Tsygannik, T.I.Mareeva, V.A.Nesmeianov, W.Pangborn, N.Lee, W.Duax, E.Siszak, V.Z.Pletnev 2000 Bioorg.Khim. 26 571 11040993
1f90 Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide. P.V.Afonin, A.V.Fokin, I.N.Tsigannik, I.Y.Mikhailova, L.V.Onoprienko, I.I.Mikhaleva, V.T.Ivanov, T.Y.Mareeva, V.A.Nesmeyanov, N.Li, W.Duax, V.Z.Pletnev 2001 Protein Sci. 10 1514 11468348
1fai Three-dimensional structure of two crystal forms of FabR19.9 from a monoclonal anti-arsonate antibody. M.B.Lascombe, P.M.Alzari, R.J.Poljak, A.Nisonoff 1992 Proc. Natl. Acad.
Sci. USA
89 9429 1409652
1fbi Crystal structure of a cross-reaction complex between Fab F9.13.7 and guinea fowl lysozyme. J.Lescar, M.Pellegrini, H.Souchon, D.Tello, R.J.Poljak, N.Peterson, M.Greene, P.M.Alzari 1995 J.Biol.Chem 270 18067 7629116
1fc1 Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. J.Deisenhofer 1981 Biochemistry 20 2361 7236608
1fcc Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG. A.E.Sauer-Eriksson, G.J.Kleywegt, M.Uhlen, T.A.Jones 1995 Structure 3 265 7788293
1fdl Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution. T.O.Fischmann, G.A.Bentley, T.N.Bhat, G.Boulot, R.A.Mariuzza, S.E.Phillips, D.Tello, R.J.Poljak 1991 J.Biol.Chem 266 12915 1712773
1fe8 Identification of the Collagen-Binding Site of the Von Willebrand Factor A3-Domain R.A.P.Romijn, B.Bouma, W.Wuyster, P.Gros, J.Kroon, J.J.Sixma, E.G.Huizinga 2001 J.Biol.Chem. 276 9985 11098050
1fgv X-ray structures of fragments from binding and nonbinding versions of a humanized anti-CD18 antibody: structural indications of the key role of VH residues 59 to 65. C.Eigenbrot, T.Gonzalez, J.Mayeda, P.Carter, W.Werther, T.Hotaling, J.Fox, J.Kessler 1994 Proteins 18 49 7908437
2fgw
1fh5 The Crystal Structure of the Fab Fragment of the Monoclonal Antibody Mak33. Implications for Folding and Interaction with the Chaperone Bip J.G.Augustine, A.De La Calle, G.Knarr, J.Buchner, C.A.Frederick 2001 J.Biol.Chem. 276 3287 11036070
1fig Routes to catalysis: structure of a catalytic antibody and comparison with its natural counterpart. M.R.Haynes, E.A.Stura, D.Hilvert, I.A.Wilson 1994 Science 263 646 8303271
1fj1 Structural Identification of a Key Protective B-Cell Epitope in Lyme Disease Antigen OspA W.Ding, X.Huang, X.Yang, J.J.Dunn, B.J.Luft, S.Koide, C.L.Lawson 2000 J.Mol.Biol. 302 1153 11183781
1fl3 Blue-Fluorescent Antibodies A.Simeonov, M.Matsushita, E.A.Juban, E.H.Thompson, T.Z.Hoffmann, A.E.Beuscher Iv, M.J.Taylor, P.Wirsching, W.Rettig, J.K.Mccusker, R.C.Stevens, D.P.Millar, P.G.Schultz, R.A.Lerner, K.D.Janda 2000 Science 290 307 11030644
1flr 1.85 A structure of anti-fluorescein 4-4-20 Fab. M.Whitlow, A.J.Howard, J.F.Wood, E.W.Voss, K.D.Hardman 1995 Protein Eng 8 749 8637844
1fns von Willebrand factor conformation and adhesive function is modulated by an internalized water molecule. R.Celikel, Z.M.Ruggeri, K.I.Varughese 2000 Nat.Struct.Biol. 7 881 11017197
1for Structure determination of an Fab fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex. H.Liu, T.J.Smith, W.M.Lee, A.G.Mosser, R.R.Rueckert, N.H.Olson, R.H.Cheng, T.S.Baker 1994 J.Mol.Biol. 240 127 8027997
1fp5 Structure of the Human Ige-Fc Cepsilon3-Cepsilon4 Reveals Conformational Flexibility in the Antibody Effector Domains. B.A.Wurzburg, S.G.Garman, T.S.Jardetzky 2000 Immunity 13 375 11021535
1fpt Structure of the complex between the Fab fragment of a neutralizing antibody for type 1 poliovirus and its viral epitope. M.W.Wien, D.J.Filman, E.A.Stura, S.Guillot, F.Delpeyroux, R.Crainic, J.M.Hogle 1995 Nat. Struct. Biol. 2 232 7539711
1frg Crystal structure of a peptide complex of anti-influenza peptide antibody Fab 26/9. Comparison of two different antibodies bound to the same peptide antigen. M.E.Churchill, E.A.Stura, C.Pinilla, J.R.Appel, R.A.Houghten, D.H.Kono, R.S.Balderas, G.G.Fieser, U.Schulze-Gahmen, I.A.Wilson 1994 J.Mol.Biol. 241 534 7520084
1fsk Dominant epitopes and allergic cross-reactivity: complex formation between a Fab fragment of a monoclonal murine IgG antibody and the major allergen from birch pollen Bet v 1. O.Mirza, A.Henriksen, H.Ipsen, J.Larsen, M.Wissenbach, M.Spangfort, M.Gajhede 2000 J.Immunol. 165 331 10861069
1fvb Model-building study of the combining sites of two antibodies to alpha (1----6)dextran. E.A.Padlan, E.A.Kabat 1988 Proc. Natl. Acad.
Sci. USA
85 6885 2457920
1fvw
2fvb
2fvw
1fvc X-ray structures of the antigen-binding domains from three variants of humanized anti-p185HER2 antibody 4D5 and comparison with molecular modeling. C.Eigenbrot, M.Randal, L.Presta, P.Carter, A.A.Kossiakoff 1993 J.Mol.Biol. 229 969 8095303
1fvd
1fve
1g6v Antigen specificity and high affinity binding provided by one single loop of a camel single-domain antibody. A.Desmyter, K.Decanniere, S.Muyldermans, L.Wyns 2001 J.Biol.Chem. 276 26285 11342547
1g7h Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface. E.J.Sundberg, M.Urrutia, B.C.Braden, J.Isern, D.Tsuchiya, B.A.Fields, E.L.Malchiodi, J.Tormo, F.P.Schwarz, R.A.Mariuzza 2000 Biochemistry 39 15375 11112523
1g7i
1g7j
1g7l
1g7m
1g84 The structure of the IgE Cepsilon2 domain and its role in stabilizing the complex with its high-affinity receptor FcepsilonRIalpha. J.M.Mcdonnell, D.Cowburn, H.J.Gould, B.J.Sutton, R.Calvert, R.E.Beavil, A.J.Beavil, A.J.Henry 2001 Nat.Struct.Biol. 8 437 11323720
1g8q CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs. K.Kitadokoro, D.Bordo, G.Galli, R.Petracca, F.Falugi, S.Abrignani, G.Grandi, M.Bolognesi 2001 EMBO J. 20 12 11226150
1g9m Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. P.D.Kwong, R.Wyatt, S.Majeed, J.Robinson, R.W.Sweet, J.Sodroski, W.A.Hendrickson 2000 Structure 8 1329 11188697
1g9n Structures of HIV-1 Gp120 Envelope Glycoproteins from Laboratory-Adapted and Primary Isolates P.D.Kwong, R.Wyatt, S.Majeed, J.Robinson, R.W.Sweet, J.Sodroski, W.A.Hendrickson 2000 Structure 8 1329 11188697
1gaf The immunological evolution of catalysis. P.A.Patten, N.S.Gray, P.L.Yang, C.B.Marks, G.J.Wedemayer, J.J.Boniface, R.C.Stevens, P.G.Schultz 1996 Science 271 1086 8599084
1gc1 Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. P.D.Kwong, R.Wyatt, J.Robinson, R.W.Sweet, J.Sodroski, W.A.Hendrickson 1998 Nature 393 648 9641677
1ggb Major antigen-induced domain rearrangements in an antibody. R.L.Stanfield, M.Takimoto-Kamimura, J.M.Rini, A.T.Profy, I.A.Wilson 1993 Structure 1 83 8069628
1ggc
1ggi Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody, 50.1, in complex with its V3 loop peptide antigen. J.M.Rini, R.L.Stanfield, E.A.Stura, P.A.Salinas, A.T.Profy, I.A.Wilson 1993 Proc. Natl. Acad.
Sci. USA
90 6325 8327513
1ghf Crystal structure of an anti-anti-idiotype shows it to be self-complementary. N.Ban, J.Day, X.Wang, S.Ferrone, A.McPherson 1996 J.Mol.Biol. 255 617 8568901
1ghl Crystal structures of pheasant and guinea fowl egg-white lysozymes. J.Lescar, H.Souchon, P.M.Alzari 1994 Protein Sci. 3 788 8061608
1hhl
1gig Refined three-dimensional structure of the Fab fragment of a murine IgGl,lambda antibody. T.Bizebard, R.Daniels, R.Kahn, B.Golinellipimpaneau, J.J.Skehel, M.Knossow 1994 Acta Crystallogr D
Biol Crystallogr
50 768 15299376
1gpo The rational construction of an antibody against cystatin: lessons from the crystal structure of an artificial Fab fragment. W.Schiweck, A.Skerra 1997 J.Mol.Biol. 268 934 9180382
1h8n The importance of framework residues H6, H7 and H10 in antibody heavy chains: experimental evidence for a new structural subclassification of antibody V(H) domains. S.Jung, S.Spinelli, B.Schimmele, A.Honegger, L.Pugliese, C.Cambillau, A.Pluckthun 2001 J.Mol.Biol. 309 701 11397090
1h8o Selection, characterization and x-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries. J.Burmester, S.Spinelli, L.Pugliese, A.Krebber, A.Honegger, S.Jung, B.Schimmele, C.Cambillau, A.Pluckthun 2001 J.Mol.Biol. 309 671 11397088
1h8s
1hcv The crystal structure of a llama heavy chain variable domain. S.Spinelli, L.Frenken, D.Bourgeois, L.de Ron, W.Bos, T.Verrips, C.Anguille, C.Cambillau, M.Tegoni 1996 Nat. Struct. Biol. 3 752 7874347
1hez Complex between Peptostreptococcus magnus protein L and a human antibody reveals structural convergence in the interaction modes of Fab binding proteins. M.Graille, E.A.Stura, N.G.Housden, J.A.Beckingham, S.P.Bottomley, D.Beale, M.J.Taussig, B.J.Sutton, M.G.Gore, J.B.Charbonnier 2001 Structure
(London)
9 679 11587642
1hf4 Structural effects of monovalent anions on polymorphic lysozyme crystals. M.C.Vaney, I.Broutin, P.Retailleau, A.Douangamath, S.Lafont, C.Hamiaux, T.Prange, A.Ducruix, M.Ries-Kautt 2001 Acta Crystallogr.,
Sect.D
57 929 11418760
1hfm A three-dimensional model of an anti-lysozyme antibody. S.J.Smith-Gill, C.Mainhart, T.B.Lavoie, R.J.Feldmann, W.Drohan, B.R.Brooks 1987 J.Mol.Biol. 194 713 3656404
2hfm
1hgd Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic acid: analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography. N.K.Sauter, J.E.Hanson, G.D.Glick, J.H.Brown, R.L.Crowther, S.J.Park, J.J.Skehel, D.C.Wiley 1992 Biochemistry 31 9609 1327122
1hge
1hgf
1hgg
1hgh
1hgi
1hgj
1hh6 Evolutionary transition pathways for changing peptide ligand specificity and structure. U.Hoffmuller, T.Knaute, M.Hahn, W.Hohne, J.Schneider-Mergener, A.Kramer 2000 EMBO J. 19 4866 10990450
1hh9
1hi6 Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity. T. Keitel, A. Kramer, H. Wessner, C. Scholz, J. Schneider-Mergener, W. Hohne 1997 Cell 91 811 9413990
1hil Structural evidence for induced fit as a mechanism for antibody-antigen recognition. J.M.Rini, U.Schulze-Gahmen, I.A.Wilson 1992 Science 255 959 1546293
1him
1hin
1hkl Crystal structures of the free and liganded form of an esterolytic catalytic antibody. G.J.Wedemayer, L.H.Wang, P.A.Patten, P.G.Schultz, R.C.Stevens 1997 J.Mol.Biol. 268 390 9159478
1hmr Structural studies on human muscle fatty acid binding protein at 1.4 A resolution: binding interactions with three C18 fatty acids. A.C.Young, G.Scapin, A.Kromminga, S.B.Patel, J.H.Veerkamp, J.C.Sacchettini 1994 Structure 2 523 7922029
1hms
1hmt
1hni Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution. J.Ding, K.Das, C.Tantillo, W.Zhang, A.D.Clark Jr., S.Jessen, X.Lu, Y.Hsiou, A.Jacobo-Molina, K.Andries, et al. 1995 Structure 3 365 7542140
1hnv Structure of HIV-1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors. J.Ding, K.Das, H.Moereels, L.Koymans, K.Andries, P.A.Janssen, S.H.Hughes, E.Arnold 1995 Nat. Struct. Biol. 2 407 7545077
1hou Structural requirements of the major protective antibody to Haemophilus influenzae type b. L.Hougs, L.Juul, A.Svejgaard, T.Barington 1999 Infect Immun. 67 2503 10225914
1hys Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. S.G.Sarafianos, K.Das, C.Tantillo, A.D.Clark Jr., J.Ding, J.Whitcomb, P.L.Boyer, S.H.Hughes, E.Arnold 2001 EMBO J. 20 1449 11250910
2dqt Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis. O.Kristensen, D.G.Vassylyev, F.Tanaka, K.Morikawa, I.Fujii 2007 J.Mol.Biol. 369 198 17428500
2dqu
1hzh Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design. E.O.Saphire, P.W.H.I.Parren, R.Pantophlet, M.B.Zwick, G.M.Morris, P.M.Rudd, R.A.Dwek, R.L.Stanfield, D.R.Burton, I.A.Wilson 2001 Science 239 1155 11498595
1hzp Crystal structure of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III J.N.Scarsdale, G.Kazanina, X.He, K.A.Reynolds, H.T.Wright 2001 J.Biol.Chem. 276 20516 11278743
1i3u Lateral recognition of a dye hapten by a llama VHH domain. S.Spinelli, M.Tegoni, L.Frenken, C.Van Vliet, C.Cambillau 2001 J.Mol.Biol. 311 123 11469862
1i3v
1i7z Crystal structure of a cocaine-binding antibody. N.A.Larsen, B.Zhou, A.Heine, P.Wirsching, K.D.Janda, I.A.Wilson 2001 J.Mol.Biol. 311 9 11469854
1iai Crystal structure of an idiotype-anti-idiotype Fab complex. N.Ban, C.Escobar, R.Garcia, K.Hasel, J.Day, A.Greenwood, A.McPherson 1994 Proc. Natl. Acad.
Sci. USA
91 1604 8127852
1ibg Structure and specificity of the anti-digoxin antibody 40-50. P.D.Jeffrey, J.F.Schildbach, C.Y.Chang, P.H.Kussie, M.N.Margolies, S.Sheriff 1995 J.Mol.Biol. 248 344 7739045
1ic4 Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex. M.Shiroishi, A.Yokota, K.Tsumoto, H.Kondo, Y.Nishimiya, K.Horii, M.Matsushima, K.Ogasahara, K.Yutani, I.Kumagai 2001 J.Biol.Chem. 276 23042 11297547
1ic5
1ic7
1ifb Refined apoprotein structure of rat intestinal fatty acid binding protein produced in Escherichia coli. J.C.Sacchettini, J.I.Gordon, L.J.Banaszak 1989 Proc. Natl. Acad.
Sci. USA
86 7736 2682622
1ifh Detailed analysis of the free and bound conformations of an antibody. X-ray structures of Fab 17/9 and three different Fab-peptide complexes. U.Schulze-Gahmen, J.M.Rini, I.A.Wilson 1993 J.Mol.Biol. 234 1098 8263915
1igc The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab. J.P.Derrick, D.B.Wigley 1994 J.Mol.Biol. 243 906 7966308
1igf Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A. R.L.Stanfield, T.M.Fieser, R.A.Lerner, I.A.Wilson 1990 Science 248 712 2333521
2igf
1igi 26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity. P.D.Jeffrey, R.K.Strong, L.C.Sieker, C.Y.Chang, R.L.Campbell, G.A.Petsko, E.Haber, M.N.Margolies, S.Sheriff 1993 Proc. Natl. Acad.
Sci. USA
90 10310 8234291
1igj
1igt Refined structure of an intact IgG2a monoclonal antibody. L.J.Harris, S.B.Larson, K.W.Hasel, A.McPherson 1997 Biochemistry 36 1581 9048542
1igy Crystallographic structure of an intact IgG1 monoclonal antibody. L.J.Harris, E.Skaletsky, A.McPherson 1998 J.Mol.Biol. 275 861 9480774
1iif Structural base of the interaction of a monoclonal antibody against p24 of HIV-1 with its peptide epitope. W.E.Hoehne, G.Kuttner, S.Kiebig, G.Hausdorf, R.Grunow, K.Winkler, H.Wessner, E.Giebmann, R.Stigler, J.Schneider-Mergener, R.V.Baehr, D.Schomburg 1993 Mol.Immunol. 30 1213 7692237
1iis The structure of a human type III Fcgamma receptor in complex with Fc. S.Radaev, S.Motyka, W.-H.Fridman, C.Sautes-Fridman, P.D.Sun 2001 J.Biol.Chem. 276 16469 11297532
1iix
1ikf A conformation of cyclosporin A in aqueous environment revealed by the X-ray structure of a cyclosporin-Fab complex. D.Altschuh, O.Vix, B.Rees, J.C.Thierry 1992 Science 256 92 1566062
1il1 Structure of an anti-HIV monoclonal Fab antibody fragment specific to a gp120 C-4 region peptide. M.B.Berry, K.A.Johnson, W.Radding, M.Fung, R.Liou, G.N.Phillips Jr. 2001 Proteins Struct.
Funct. Genet.
45 281 11599031
1ind How the anti-(metal chelate) antibody CHA255 is specific for the metal ion of its antigen: X-ray structures for two Fab'/hapten complexes with different metals in the chelate. R.A.Love, J.E.Villafranca, R.M.Aust, K.K.Nakamura, R.A.Jue, J.G.Major Jr., R.Radhakrishnan, W.F.Butler 1993 Biochemistry 32 10950 8218161
1ine
1iqd Structure of a factor VIII C2 domain-immunoglobulin G4kappa Fab complex: identification of an inhibitory antibody epitope on the surface of factor VIII. P.C.Spiegel Jr., M.Jacquemin, J.M.Saint-Remy, B.L.Stoddard, K.P.Pratt 2001 Blood 98 13 11418455
1ivl The de novo design of an antibody combining site. Crystallographic analysis of the VL domain confirms the structural model. L.O.Essen, A.Skerra 1994 J.Mol.Biol. 238 226 8158652
1jhl Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex. V.Chitarra, P.M.Alzari, G.A.Bentley, T.N.Bhat, J.L.Eisele, A.Houdusse, J.Lescar, H.Souchon, R.J.Poljak 1993 Proc. Natl. Acad.
Sci. USA
90 7711 8356074
1jrh Neutralizing epitopes on the extracellular interferon gamma receptor (IFNgammaR) alpha-chain characterized by homolog scanning mutagenesis and X-ray crystal structure of the A6 fab-IFNgammaR1-108 complex. S.Sogabe, F.Stuart, C.Henke, A.Bridges, G.Williams, A.Birch, F.K.Winkler, J.A.Robinson 1997 J.Mol.Biol. 273 882 9367779
1kb5 The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain. D.Housset, G.Mazza, C.Gregoire, C.Piras, B.Malissen, J.C.Fontecilla-Camps 1997 EMBO J. 16 4205 9250664
1kel Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution. L.C.Hsieh-Wilson, P.G.Schultz, R.C.Stevens 1996 Proc. Natl. Acad.
Sci. USA
93 5363 8643580
1kem
1kip Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme. B.A.Fields, F.A.Goldbaum, W.Dall'Acqua, E.L.Malchiodi, A.Cauerhff, F.P.Schwarz, X.Ysern, R.J.Poljak, R.A.Mariuzza 1996 Biochemistry 35 15494 8952503
1kiq
1kir
1kno Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies. J.B.Charbonnier, E.Carpenter, B.Gigant, B.Golinelli-Pimpaneau, Z.Eshhar, B.S.Green, M.Knossow 1995 Proc. Natl. Acad.
Sci. USA
92 11721 8524836
1lfo The crystal structure of the liver fatty acid-binding protein. A complex with two bound oleates. J.Thompson, N.Winter, D.Terwey, J.Bratt, L.Banaszak 1997 J.Biol.Chem 272 7140 9054409
1lmk Crystal structure of a diabody, a bivalent antibody fragment. O.Perisic, P.A.Webb, P.Holliger, G.Winter, R.L.Williams 1994 Structure 2 1217 7704531
1maj Solution structure of an isolated antibody VL domain. K.L.Constantine, M.S.Friedrichs, W.J.Metzler, M.Wittekind, P.Hensley, L.Mueller 1994 J.Mol.Biol. 236 310 8107112
1mak
1mam Crystal structure to 2.45 A resolution of a monoclonal Fab specific for the Brucella A cell wall polysaccharide antigen. D.R.Rose, M.Przybylska, R.J.To, C.S.Kayden, R.P.Oomen, E.Vorberg, N.M.Young, D.R.Bundle 1993 Protein Sci. 2 1106 8358294
1mcp Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A. Y.Satow, G.H.Cohen, E.A.Padlan, D.R.Davies 1986 J.Mol.Biol. 190 593 3097327
1mel Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme. A.Desmyter, T.R.Transue, M.A.Ghahroudi, M.H.Thi, F.Poortmans, R.Hamers, S.Muyldermans, L.Wyns 1996 Nat. Struct. Biol. 3 803 8784355
1mf2 Three-dimensional structure of an Fab-peptide complex: structural basis of HIV-1 protease inhibition by a monoclonal antibody. J.Lescar, R.Stouracova, M.M.Riottot, V.Chitarra, J.Brynda, M.Fabry, M.Horejsi, J.Sedlacek, G.A.Bentley 1997 J.Mol.Biol. 267 1207 9150407
2hrp
1mfa Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution. A.Zdanov, Y.Li, D.R.Bundle, S.J.Deng, C.R.MacKenzie, S.A.Narang, N.M.Young, M.Cygler 1994 Proc. Natl. Acad.
Sci. USA
91 6423 7517550
1mfb Recognition of a carbohydrate antigenic determinant of Salmonella by an antibody. M.Cygler, S. Wu, A.Zdanov, D.R. Bundle, D.R. Rose 1993 Biochem. Soc. Trans. 21 437 7689495
1mfc
1mfd Solution structure of a trisaccharide-antibody complex: comparison of NMR measurements with a crystal structure. D.R.Bundle, H.Baumann, J.R.Brisson, S.M.Gagne, A.Zdanov, M.Cygler 1994 Biochemistry 33 5183 8172893
1mfe Recognition of a cell-surface oligosaccharide of pathogenic Salmonella by an antibody Fab fragment. M.Cygler, D.R.Rose, D.R.Bundle 1991 Science 253 442 1713710
1mig Catalytic antibody model and mutagenesis implicate arginine in transition-state stabilization. V.A.Roberts, J.Stewart, S.J.Benkovic, E.D.Getzoff 1994 J.Mol.Biol. 235 1098 8289310
1mim Structure of the Fab fragment of SDZ CHI621: A chimeric antibody against CD25. V.Mikol 1996 Acta Crystallogr D
Biol Crystallogr
52 534 15299676
1mlb Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. B.C.Braden, H.Souchon, J.L.Eisele, G.A.Bentley, T.N.Bhat, J.Navaza, R.J.Poljak 1994 J.Mol.Biol. 243 767 7966295
1mlc
1mnu Bactericidal antibody recognition of meningococcal PorA by induced fit. Comparison of liganded and unliganded Fab structures. J.van den Elsen, L.Vandeputte-Rutten, J.Kroon, P.Gros 1999 J.Biol.Chem 274 1495 9880525
1mpa Bactericidal antibody recognition of a PorA epitope of Neisseria meningitidis: crystal structure of a Fab fragment in complex with a fluorescein-conjugated peptide. J.M.van den Elsen, J.N.Herron, P.Hoogerhout, J.T.Poolman, E.Boel, T.Logtenberg, J.Wilting, D.J.Crommelin, J.Kroon, P.Gros 1997 Proteins 29 113 9294871
1mrc Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes. P.R.Pokkuluri, F.Bouthillier, Y.Li, A.Kuderova, J.Lee, M.Cygler 1994 J.Mol.Biol. 243 283 7523684
1mrd
1mre
1mrf
1nca Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex. W.R.Tulip, J.N.Varghese, W.G.Laver, R.G.Webster, P.M.Colman 1992 J.Mol.Biol. 227 122 1381757
1ncd
1ncb Crystal structures of two mutant neuraminidase-antibody complexes with amino acid substitutions in the interface. W.R.Tulip, J.N.Varghese, R.G.Webster, W.G.Laver, P.M.Colman 1992 J.Mol.Biol. 227 149 1522584
1ncc
1nfd Atomic structure of an alphabeta T cell receptor (TCR) heterodimer in complex with an anti-TCR fab fragment derived from a mitogenic antibody. J.Wang, K.Lim, A.Smolyar, M.Teng, J.Liu, A.G.Tse, J.Liu, R.E.Hussey, Y.Chishti, C.T.Thomson, R.M.Sweet, S.G.Nathenson, H.C.Chang, J.C.Sacchettini, E.L.Reinherz 1998 EMBO J 17 10 9427737
1ngp Three-dimensional structures of the Fab fragment of murine N1G9 antibody from the primary immune response and of its complex with (4-hydroxy-3-nitrophenyl)acetate. R.Mizutani, K.Miura, T.Nakayama, I.Shimada, Y.Arata, Y.Satow 1995 J.Mol.Biol. 254 208 7490744
1ngq
1nld Structure of the Fab fragment from a neutralizing monoclonal antibody directed against an epitope of gp41 from HIV-1. C.Davies, J.C.Beauchamp, D.Emery, A.Rawas, H.Muirhead 1997 Acta Crystallogr D
Biol Crystallogr
53 186 15299953
1nma N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free energy calculations capture specificity trends observed with mutant binding data. W.R.Tulip, V.R.Harley, R.G.Webster, J.Novotny 1994 Biochemistry 33 7986 7517697
1nmb The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody. R.L.Malby, W.R.Tulip, V.R.Harley, J.L.McKimm-Breschkin, W.G.Laver, R.G.Webster, P.M.Colman 1994 Structure 2 733 7994573
1nqb The 2.0-A resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3. X.Y.Pei, P.Holliger, A.G.Murzin, R.L.Williams 1997 Proc. Natl. Acad.
Sci. USA
94 9637 9275175
1nsn The crystal structure of the antibody N10-staphylococcal nuclease complex at 2.9 A resolution. P.Bossart-Whitaker, C.Y.Chang, J.Novotny, D.C.Benjamin, S.Sheriff 1995 J.Mol.Biol. 253 559 7473734
1oak Crystal structure of the von Willebrand factor A1 domain in complex with the function blocking NMC-4 Fab. R.Celikel, K.I.Varughese, ?.Madhusudan, A.Yoshioka, J.Ware, Z.M.Ruggeri 1998 Nat. Struct. Biol. 5 189 9501911
1obe Interaction between a Fab fragment against gp41 of human immunodeficiency virus 1 and its peptide epitope: characterization using a peptide epitope library and molecular modeling. R.D.Stigler, F.Ruker, D.Katinger, G.Elliott, W.Hohne, P.Henklein, J.X.Ho, K.Keeling, D.C.Carter, E.Nugel, et al. 1995 Protein Eng. 8 471 8532669
1opg Crystal structure of the OPG2 Fab. An antireceptor antibody that mimics an RGD cell adhesion site. R.Kodandapani, B.Veerapandian, T.J.Kunicki, K.R.Ely 1995 J.Biol.Chem 270 2268 7836460
1osp Crystal structure of Lyme disease antigen outer surface protein A complexed with an Fab. H.Li, J.J.Dunn, B.J.Luft, C.L.Lawson 1997 Proc. Natl. Acad.
Sci. USA
94 3584 9108020
1paj NMR solution structure and flexibility of a peptide antigen representing the receptor binding domain of Pseudomonas aeruginosa. C.McInnes, F.D.Sonnichsen, C.M.Kay, R.S.Hodges, B.D.Sykes 1993 Biochemistry 32 13432 8257679
1pak
1plg Evidence for the extended helical nature of polysaccharide epitopes. The 2.8 A resolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for alpha-(2-->8)-polysialic acid. S.V.Evans, B.W.Sigurskjold, H.J.Jennings, J.R.Brisson, R.To, W.C.Tse, E.Altman, M.Frosch, C.Weisgerber, H.D.Kratzin, et al. 1995 Biochemistry 34 6737 7538787
1psk The crystal structure of a Fab fragment to the melanoma-associated GD2 ganglioside. S.L.Pichla, R.Murali, R.M.Burnett 1997 J Struct Biol 119 6 9216084
2psk
1qbl Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution. S.E.Mylvaganam, Y.Paterson, E.D.Getzoff 1998 J.Mol.Biol. 281 301 9698550
1qbm
1wej
1qd0 Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens S.Spinelli, L.G.J.Frenken, P.Hermans, T.Verrips, K.Brown, M.Tegoni, C.Cambillau 2000 Biochemistry 39 1217 10684599
1qe1 Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids. S.G.Sarafianos, K.Das, J.Ding, S.H.Hughes, E.Arnold 1999 Proc. Natl. Acad.
Sci. USA
96 10027 10468556
1qfu A complex of influenza hemagglutinin with a neutralizing antibody that binds outside the virus receptor binding site. D.Fleury, B.Barrere, T.Bizebard, R.S.Daniels, J.J.Skehel, M.Knossow 1999 Nat. Struct. Biol. 6 530 10360354
1qfw Crystal structure of a ternary complex between human chorionic gonadotropin (hCG) and two Fv fragments specific for the alpha and beta-subunits. M.Tegoni, S.Spinelli, M.Verhoeyen, P.Davis, C.Cambillau 1999 J.Mol.Biol. 289 1375 10373373
1qgc Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop. E.A.Hewat, N.Verdaguer, I.Fita, W.Blakemore, S.Brookes, A.King, J.Newman, E.Domingo, M.G.Mateu, D.I.Stuart 1997 EMBO J. 16 1492 9130694
1qkz Crystal structure of an Fab fragment in complex with a meningococcal serosubtype antigen and a protein G domain. J.P.Derrick, I.M.Feavers, M.C.J.Maiden 1999 J.Mol.Biol. 293 81 10512717
1qle The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction. A.Harrenga, H.Michel 1999 J.Biol.Chem. 274 33296 10559205
1qlr Three-dimensional structure of the Fab from a human IgM cold agglutinin. A.Cauerhff, B.C.Braden, J.G.Carvalho, R.Aparicio, I.Polikarpov, J.Leoni, F.A.Goldman 2000 J.Immunol. 165 6422 11086081
1qnz NMR structure of an anti-gp120 antibody complex with a V3 peptide reveals a surface important for co-receptor binding. V.Tugarinov, A.Zvi, R.Levy, Y.Hayek, S.Matsushita, J.Anglister 2000 Structure Fold Des. 8 385 10801487
1qok Crystal structure of the anti-(carcinoembryonic antigen) single-chain Fv antibody MFE-23 and a model for antigen binding based on intermolecular contacts. M.K.Boehm, A.L.Corper, T.Wan, M.K.Sohi, B.J.Sutton, J.D.Thornton, P.A.Keep, K.A.Chester, R.H.J.Begent, S.J.Perkins 2000 Biochem.J. 346 519 10677374
1qp1 Molecular structure of the amyloid-forming protein kappa I Bre. L.K.Steinrauf, M.Y.Chiang, D.Shiuan 1999 J.Biochem.(Tokyo) 125 422 9990143
1rmd Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. S.F.Bellon, K.K.Rodgers, D.G.Schatz, J.E.Coleman, T.A.Steitz 1997 Nat. Struct. Biol. 4 586 9228952
1rmf Structure of a monoclonal anti-ICAM-1 antibody R6.5 Fab fragment at 2.8 A resolution. M.J.Jedrzejas, J.Miglietta, J.A.Griffin, M.Luo 1995 Acta Crystallogr D
Biol Crystallogr
51 380 15299305
1rvf Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon. T.J.Smith, E.S.Chase, T.J.Schmidt, N.H.Olson, T.S.Baker 1996 Nature 383 350 8848050
1sbs Structure of an Fab fragment against a C-terminal peptide of hCG at 2.0 A resolution. C.Fotinou, J.Beauchamp, P.Emsley, A.deHaan, W.J.Schielen, E.Bos, N.W.Isaacs 1998 J.Biol.Chem 273 22515 9712877
1sm3 Crystal structure at 1.95 A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition. P.Dokurno, P.A.Bates, H.A.Band, L.M.D.Stewart, J.M.Lally, J.M.Burchell, J.Taylor-Papadimitriou, D.Snary, M.J.E.Sternberg, P.S.Freemont 1998 J.Mol.Biol. 284 713 9826510
1tet Crystal structure of an anticholera toxin peptide complex at 2.3 A. M.Shoham 1993 J.Mol.Biol. 232 1169 7690406
1tor Compared structures of the free nicotinic acetylcholine receptor main immunogenic region (MIR) decapeptide and the antibody-bound [A76]MIR analogue: a molecular dynamics simulation from two-dimensional NMR data. P.Orlewski, M.Marraud, M.T.Cung, V.Tsikaris, M.Sakarellos-Daitsiotis, C.Sakarellos, E.Vatzaki, S.J.Tzartos 1996 Biopolymers 40 419 9062066
1tos
1ucb X-ray structure of the uncomplexed anti-tumor antibody BR96 and comparison with its antigen-bound form. S.Sheriff, C.Y.Chang, P.D.Jeffrey, J.Bajorath 1996 J.Mol.Biol. 259 938 8683596
1ure The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm. M.E.Hodsdon, J.W.Ponder, D.P.Cistola 1996 J.Mol.Biol. 264 585 8969307
1vfa Bound water molecules and conformational stabilization help mediate an antigen-antibody association. T.N.Bhat, G.A.Bentley, G.Boulot, M.I.Greene, D.Tello, W.Dall'Acqua, H.Souchon, F.P.Schwarz, R.A.Mariuzza, R.J.Poljak 1994 Proc. Natl. Acad.
Sci. USA
91 1089 8302837
1vfb
1vge Structural studies of human autoantibodies. Crystal structure of a thyroid peroxidase autoantibody Fab. S.Chacko, E.A.Padlan, S.Portolano, S.M.McLachlan, B.Rapoport 1996 J.Biol.Chem 271 12191 8647813
1vhp Rearrangement of the former VL interface in the solution structure of a camelised, single antibody VH domain. L.Riechmann 1996 J.Mol.Biol. 259 957 8683598
1yec Structural convergence in the active sites of a family of catalytic antibodies. J.B.Charbonnier, B.Golinelli-Pimpaneau, B.Gigant, D.S.Tawfik, R.Chap, D.G.Schindler, S.H.Kim, B.S.Green, Z.Eshhar, M.Knossow 1997 Science 275 1140 9027317
1yed
1yee
1yef X-ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release. B.Gigant, J.B.Charbonnier, Z.Eshhar, B.S.Green, M.Knossow 1997 Proc. Natl. Acad.
Sci. USA
94 7857 9223277
1yeg
1yeh
1yei Crossreactivity, efficiency and catalytic specificity of an esterase-like antibody. B.Gigant, J.Charbonnier, Z.Eshhar, B.S.Green, M.Knossow 1998 J.Mol.Biol. 284 741 9826512
1yej
1yek
1yuh Structural analysis of affinity maturation: the three-dimensional structures of complexes of an anti-nitrophenol antibody. S.C.Yuhasz, C.Parry, M.Strand, L.M.Amzel 1995 Mol Immunol 32 1143 8544863
25c8 Structural basis for antibody catalysis of a disfavored ring closure reaction. K.Gruber, B.Zhou, K.N.Houk, R.A.Lerner, C.G.Shevlin, I.A.Wilson 1999 Biochemistry 38 7062 10353817
35c8
2ans Studies of the ligand binding reaction of adipocyte lipid binding protein using the fluorescent probe 1, 8-anilinonaphthalene-8-sulfonate. J.J. Ory, L.J. Banaszak 1999 Biophys.J. 77 1107 10423455
2ap2 Antibody C219 recognizes an alpha-helical epitope on P-glycoprotein. J.M.H.Vandenelsen, D.A.Kuntz, D.R.Rose 1999 Proc. Natl. Acad.
Sci. USA
55 13679 10570132
2f19 Three-dimensional structure of two crystal Forms of fabR19.9 from a monoclonal anti-arsonate antibody M.-B.Lascombe, P.M.Alzari, R.J.Poljak, A.Nisonoff 1992 Proc. Natl. Acad.
Sci. USA
89 9429 1409652
2fb4 Die Primaerstruktur Des Kristallisierbaren Monoklonalen Immunoglobulins Igg1 Kol. II. Aminosaeuresequenz Der L-Kette, Lambda-Typ, Subgruppe I (German) H.D.Kratzin, W.Palm, M.Stangel, W.E.Schmidt, J.Friedrich, N.Hilschmann 1989 Biol. Chem.
Hoppe-Seyler
370 263 2713105
2ig2
2fbj Refined Crystal Structure of the Galactan-Binding Immunoglobulin Fab J539 at 1.95-Angstroms Resolution T.N.Bhat, E.A.Padlan, D.R.Davies n/a To be Published n/a n/a n/a
2frt Computational determination of the structure of rat Fc bound to the neonatal Fc receptor. Z.Weng, K.Gulukota, D.E.Vaughn, P.J.Bjorkman, C.DeLisi 1998 J.Mol.Biol. 282 217 9735282
2gfb Crystal structure of a catalytic antibody Fab with esterase-like activity. B.Golinelli-Pimpaneau, B.Gigant, T.Bizebard, J.Navaza, P.Saludjian, R.Zemel, D.S.Tawfik, Z.Eshhar, B.S.Green, M.Knossow 1994 Structure 2 175 8069632
2h1p The three-dimensional structures of a polysaccharide binding antibody to Cryptococcus neoformans and its complex with a peptide from a phage display library: implications for the identification of peptide mimotopes. A.C.M.Young, P.Valadon, A.Casadevall, M.D.Scharff, J.C.Sacchettini 1997 J.Mol.Biol. 274 622 9417940
2hmb Three-dimensional structure of recombinant human muscle fatty acid-binding protein. G.Zanotti, G.Scapin, P.Spadon, J.H.Veerkamp, J.C.Sacchettini 1992 J.Biol.Chem 267 18541 1526991
2hmg Refinement of the influenza virus hemagglutinin by simulated annealing. W.I.Weis, A.T.Brunger, J.J.Skehel, D.C.Wiley 1990 J.Mol.Biol. 212 737 2329580
3hmg
4hmg
5hmg
2hmi Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 angstroms resolution. J.Ding, K.Das, H.Yu, S.G.Sarafianos, A.D.Clark Junior, A.Jacobo-Molina, C.Tantillo, S.H.Hughes, E.Arnold 1998 J.Mol.Biol. 284 1095 9837729
2ifb Crystal structure of rat intestinal fatty-acid-binding protein. Refinement and analysis of the Escherichia coli-derived protein with bound palmitate. J.C.Sacchettini, J.I.Gordon, L.J.Banaszak 1989 J.Mol.Biol. 208 327 2671390
2iff Structure of an antibody-lysozyme complex unexpected effect of conservative mutation. S.Chacko, E.Silverton, L.Kam-Morgan, S.Smith-Gill, G.Cohen, D.Davies 1995 J.Mol.Biol. 245 261 7531245
2imm Refined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant. B.Steipe, A.Pluckthun, R.Huber 1992 J.Mol.Biol. 225 739 1602480
2jel The 2.5 Angstroms resolution structure of the jel42 Fab fragment/HPr complex L.Prasad, E.B.Waygood, J.S.Lee, L.T.J.Delbaere 1998 J.Mol.Biol. 280 829 9671553
2loi Nephritogenic lambda light chain dimer: a unique human miniautoantibody against complement factor H. T.S.Jokiranta, A.Solomon, M.K.Pangburn, P.F.Zipfel, S.Meri 1999 J.Immunol. 163 4590 10510403
2mcp Refined Crystal Structure of the Mcpc603 Fab-Phosphocholine Complex at 3.1 Angstroms Resolution E.A.Padlan, G.H.Cohen, D.R.Davies n/a To be Published n/a n/a n/a
2mpa Bactericidal antibody recognition of a PorA epitope of Neisseria meningitidis: crystal structure of a Fab fragment in complex with a fluorescein-conjugated peptide. J.M.H.Van Den Elsen, J.N.Herron, P.Hoogerhout, J.T.Poolman, E.Boel, T.Logtenberg, J.Wilting, D.J.A.Crommelin, J.Kroon, P.Gros 1997 Proteins: Struct.,
Funct., Genet.
29 113 9294871
2pcp Crystal structure of monoclonal 6B5 Fab complexed with phencyclidine. K.Lim, S.M.Owens, L.Arnold, J.C.Sacchettini, D.S.Linthicum 1998 J.Biol.Chem 273 28576 9786848
2vir Antigen distortion allows influenza virus to escape neutralization. D.Fleury, S.A.Wharton, J.J.Skehel, M.Knossow, T.Bizebard 1998 Nat. Struct. Biol. 5 119 9461077
2vis
2vit
2viu
32c2 Structure of an activity suppressing Fab fragment to cytochrome P450 aromatase: insights into the antibody-antigen interactions. M.W.Sawicki, P.C.Ng, B.M.Burkhart, V.Pletnev, T.Higashiyama, Y.Osawa, D.Ghosh 1999 Mol.Immunol. 36 423 10449095
3fct Structural and kinetic evidence for strain in biological catalysis. F.E.Romesberg, B.D.Santarsiero, B.Spiller, J.Yin, D.Barnes, P.G.Schultz, R.C.Stevens 1998 Biochemistry 37 14404 9772166
3fru Structural basis of pH-dependent antibody binding by the neonatal Fc receptor. D.E.Vaughn, P.J.Bjorkman 1998 Structure 6 63 9493268
1yqv HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry. G.H.Cohen, E.W. Silverton, E.A. Padlan, F. Dyda, J.A. Wibbenmeyer, R.C. Willson, D.R.Davies 2005 Acta Crystallogr D
Biol Crystallogr
61 628 15858274
3hfm Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. E.A.Padlan, E.W.Silverton, S.Sheriff, G.H.Cohen, S.J.Smith-Gill, D.R.Davies 1989 Proc. Natl. Acad.
Sci. USA
86 5938 2762305
3ifb Solution structure of human intestinal fatty acid binding protein: implications for ligand entry and exit. F.Zhang, C.Lucke, L.J.Baier, J.C.Sacchettini, J.A.Hamilton 1997 J Biomol NMR 9 213 9204553
43c9 Structural Basis for Amide Hydrolysis Catalyzed by the 43C9 Antibody M.M.Thayer, E.H.Olender, A.S.Arvai, C.K.Koike, I.L.Canestrelli, J.D.Stewart, S.J.Benkovic, E.D.Getzoff, V.A.Roberts 1999 J.Mol.Biol. 291 329 10438624
43ca
4fab Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentanediol. J.N.Herron, X.M.He, M.L.Mason, E.W.Voss Jr., A.B.Edmundson 1989 Proteins 5 271 2508085
6fab Three-dimensional structure of murine anti-p-azophenylarsonate Fab 36- 71. 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten. R.K.Strong, R.Campbell, D.R.Rose, G.A.Petsko, J.Sharon, M.N.Margolies 1991 Biochemistry 30 3739 2015229
8fab
7fab Crystal structure of human immunoglobulin fragment Fab New refined at 2.0 A resolution. F.A.Saul, R.J.Poljak 1992 Proteins 14 363 1438175

抗体についてさらに知りたい方へ

以下の参考文献もご参照ください。

  • David R. Davies & Susan Chacko 1993 Antibody structure. Accounts of Chemical Research 26 pp.421-427
  • Life, death and the immune system, a special issue of scientific american , September 1993 .
  • David R. Davies, Eduardo A. Padlan & Steven Sheriff 1990 Antibody- antigen complexes. Annual Reviewof Biochemistry 59 pp.439-473



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