[日本語] English
万見
- PDB-8cbd: SARS-CoV-2 Delta-RBD complexed with BA.4/5-1 and EY6A Fabs -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 8cbd
タイトルSARS-CoV-2 Delta-RBD complexed with BA.4/5-1 and EY6A Fabs
要素
  • BA.4/5-1 heavy chain
  • BA.4/5-1 light chain
  • EY6A heavy chain
  • EY6A light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 / BA.4 mAb / BA.5 mAb / RBD / BA.4/5-1 / BA.4/5-2 / BA.4/5-5 / EY6A / VIRAL PROTEIN/Immune system
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.52 Å
データ登録者Zhou, D. / Ren, J. / Stuart, D.I.
資金援助 英国, 2件
組織認可番号国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 英国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
引用ジャーナル: Nat Commun / 年: 2024
タイトル: Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection.
著者: Liu, C. / Das, R. / Dijokaite-Guraliuc, A. / Zhou, D. / Mentzer, A.J. / Supasa, P. / Selvaraj, M. / Duyvesteyn, H.M.E. / Ritter, T.G. / Temperton, N. / Klenerman, P. / Dunachie, S.J. / ...著者: Liu, C. / Das, R. / Dijokaite-Guraliuc, A. / Zhou, D. / Mentzer, A.J. / Supasa, P. / Selvaraj, M. / Duyvesteyn, H.M.E. / Ritter, T.G. / Temperton, N. / Klenerman, P. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
履歴
登録2023年1月25日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年2月7日Provider: repository / タイプ: Initial release
改定 1.12024年5月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
R: Spike protein S1
H: BA.4/5-1 heavy chain
L: BA.4/5-1 light chain
E: EY6A heavy chain
F: EY6A light chain
G: EY6A heavy chain
I: EY6A light chain
J: EY6A heavy chain
K: EY6A light chain
X: Spike protein S1
A: BA.4/5-1 heavy chain
B: BA.4/5-1 light chain
Y: Spike protein S1
C: BA.4/5-1 heavy chain
D: BA.4/5-1 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)352,23716
ポリマ－352,01615
非ポリマー2211
水00
1
R: Spike protein S1
H: BA.4/5-1 heavy chain
L: BA.4/5-1 light chain
E: EY6A heavy chain
F: EY6A light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)117,5606
ポリマ－117,3395
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
G: EY6A heavy chain
I: EY6A light chain
Y: Spike protein S1
C: BA.4/5-1 heavy chain
D: BA.4/5-1 light chain


分子量 (理論値)分子数
合計 (水以外)117,3395
ポリマ－117,3395
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
J: EY6A heavy chain
K: EY6A light chain
X: Spike protein S1
A: BA.4/5-1 heavy chain
B: BA.4/5-1 light chain


分子量 (理論値)分子数
合計 (水以外)117,3395
ポリマ－117,3395
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)242.046, 139.369, 168.528
Angle α, β, γ (deg.)90.000, 115.580, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "A"
d_2ens_1chain "C"
d_3ens_1chain "H"
d_1ens_2(chain "B" and (resid 2 or resid 5 through 17...
d_2ens_2(chain "D" and (resid 2 or resid 5 through 17...
d_3ens_2(chain "F" and (resid 2 or resid 5 through 17...
d_4ens_2(chain "I" and (resid 2 or resid 5 through 17...
d_5ens_2(chain "K" and (resid 2 or resid 5 through 17...
d_6ens_2(chain "L" and (resid 2 or resid 5 through 17...
d_1ens_3chain "E"
d_2ens_3chain "G"
d_3ens_3chain "J"
d_1ens_4(chain "R" and resid 334 through 527)
d_2ens_4chain "X"
d_3ens_4chain "Y"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNCYSCYSAK1 - 2201 - 220
d_21ens_1GLNGLNCYSCYSCN1 - 2201 - 220
d_31ens_1GLNGLNCYSCYSHB1 - 2201 - 220
d_11ens_2ILEILEILEILEBL22
d_12ens_2THRTHRASPASPBL5 - 175 - 17
d_13ens_2VALVALCYSCYSBL19 - 2319 - 23
d_14ens_2ALAALASERSERBL25 - 2625 - 26
d_15ens_2ILEILESERSERBL29 - 3029 - 30
d_16ens_2LEULEULEULEUBL3333
d_17ens_2TRPTRPGLNGLNBL35 - 3835 - 38
d_18ens_2PROPROLEULEUBL40 - 4740 - 47
d_19ens_2TYRTYRTYRTYRBL4949
d_110ens_2ALAALASERSERBL51 - 5251 - 52
d_111ens_2LEULEULEULEUBL5454
d_112ens_2SERSERGLNGLNBL56 - 9056 - 90
d_113ens_2TYRTYRTYRTYRBL9292
d_114ens_2THRTHRGLYGLYBL97 - 9997 - 99
d_115ens_2GLYGLYVALVALBL101 - 104101 - 104
d_116ens_2ILEILETHRTHRBL106 - 164106 - 164
d_117ens_2GLNGLNGLUGLUBL166 - 187166 - 187
d_118ens_2HISHISTHRTHRBL189 - 206189 - 206
d_21ens_2ILEILEILEILEDO22
d_22ens_2THRTHRASPASPDO5 - 175 - 17
d_23ens_2VALVALCYSCYSDO19 - 2319 - 23
d_24ens_2ALAALASERSERDO25 - 2625 - 26
d_25ens_2ILEILESERSERDO29 - 3029 - 30
d_26ens_2LEULEULEULEUDO3333
d_27ens_2TRPTRPGLNGLNDO35 - 3835 - 38
d_28ens_2PROPROLEULEUDO40 - 4740 - 47
d_29ens_2TYRTYRTYRTYRDO4949
d_210ens_2ALAALASERSERDO51 - 5251 - 52
d_211ens_2LEULEULEULEUDO5454
d_212ens_2SERSERGLNGLNDO56 - 9056 - 90
d_213ens_2TYRTYRTYRTYRDO9292
d_214ens_2THRTHRGLYGLYDO97 - 9997 - 99
d_215ens_2GLYGLYVALVALDO101 - 104101 - 104
d_216ens_2ILEILETHRTHRDO106 - 164106 - 164
d_217ens_2GLNGLNGLUGLUDO166 - 187166 - 187
d_218ens_2HISHISTHRTHRDO189 - 206189 - 206
d_31ens_2ILEILEILEILEFE22
d_32ens_2THRTHRASPASPFE5 - 175 - 17
d_33ens_2VALVALCYSCYSFE19 - 2319 - 23
d_34ens_2ALAALASERSERFE25 - 2625 - 26
d_35ens_2ILEILESERSERFE29 - 3029 - 30
d_36ens_2LEULEULEULEUFE3333
d_37ens_2TRPTRPGLNGLNFE35 - 3835 - 38
d_38ens_2PROPROLEULEUFE40 - 4740 - 47
d_39ens_2TYRTYRTYRTYRFE4949
d_310ens_2ALAALASERSERFE51 - 5251 - 52
d_311ens_2LEULEULEULEUFE5454
d_312ens_2SERSERGLNGLNFE56 - 9056 - 90
d_313ens_2TYRTYRTYRTYRFE9292
d_314ens_2THRTHRGLYGLYFE98 - 10098 - 100
d_315ens_2GLYGLYVALVALFE102 - 105102 - 105
d_316ens_2ILEILETHRTHRFE107 - 165107 - 165
d_317ens_2GLNGLNGLUGLUFE167 - 188167 - 188
d_318ens_2HISHISTHRTHRFE190 - 207190 - 207
d_41ens_2ILEILEILEILEIG22
d_42ens_2THRTHRASPASPIG5 - 175 - 17
d_43ens_2VALVALCYSCYSIG19 - 2319 - 23
d_44ens_2ALAALASERSERIG25 - 2625 - 26
d_45ens_2ILEILESERSERIG29 - 3029 - 30
d_46ens_2LEULEULEULEUIG3333
d_47ens_2TRPTRPGLNGLNIG35 - 3835 - 38
d_48ens_2PROPROLEULEUIG40 - 4740 - 47
d_49ens_2TYRTYRTYRTYRIG4949
d_410ens_2ALAALASERSERIG51 - 5251 - 52
d_411ens_2LEULEULEULEUIG5454
d_412ens_2SERSERGLNGLNIG56 - 9056 - 90
d_413ens_2TYRTYRTYRTYRIG9292
d_414ens_2THRTHRGLYGLYIG98 - 10098 - 100
d_415ens_2GLYGLYVALVALIG102 - 105102 - 105
d_416ens_2ILEILETHRTHRIG107 - 165107 - 165
d_417ens_2GLNGLNGLUGLUIG167 - 188167 - 188
d_418ens_2HISHISTHRTHRIG190 - 207190 - 207
d_51ens_2ILEILEILEILEKI22
d_52ens_2THRTHRASPASPKI5 - 175 - 17
d_53ens_2VALVALCYSCYSKI19 - 2319 - 23
d_54ens_2ALAALASERSERKI25 - 2625 - 26
d_55ens_2ILEILESERSERKI29 - 3029 - 30
d_56ens_2LEULEULEULEUKI3333
d_57ens_2TRPTRPGLNGLNKI35 - 3835 - 38
d_58ens_2PROPROLEULEUKI40 - 4740 - 47
d_59ens_2TYRTYRTYRTYRKI4949
d_510ens_2ALAALASERSERKI51 - 5251 - 52
d_511ens_2LEULEULEULEUKI5454
d_512ens_2SERSERGLNGLNKI56 - 9056 - 90
d_513ens_2TYRTYRTYRTYRKI9292
d_514ens_2THRTHRGLYGLYKI98 - 10098 - 100
d_515ens_2GLYGLYVALVALKI102 - 105102 - 105
d_516ens_2ILEILETHRTHRKI107 - 165107 - 165
d_517ens_2GLNGLNGLUGLUKI167 - 188167 - 188
d_518ens_2HISHISTHRTHRKI190 - 207190 - 207
d_61ens_2ILEILEILEILELC22
d_62ens_2THRTHRASPASPLC5 - 175 - 17
d_63ens_2VALVALCYSCYSLC19 - 2319 - 23
d_64ens_2ALAALASERSERLC25 - 2625 - 26
d_65ens_2ILEILESERSERLC29 - 3029 - 30
d_66ens_2LEULEULEULEULC3333
d_67ens_2TRPTRPGLNGLNLC35 - 3835 - 38
d_68ens_2PROPROLEULEULC40 - 4740 - 47
d_69ens_2TYRTYRTYRTYRLC4949
d_610ens_2ALAALASERSERLC51 - 5251 - 52
d_611ens_2LEULEULEULEULC5454
d_612ens_2SERSERGLNGLNLC56 - 9056 - 90
d_613ens_2TYRTYRTYRTYRLC9292
d_614ens_2THRTHRGLYGLYLC97 - 9997 - 99
d_615ens_2GLYGLYVALVALLC101 - 104101 - 104
d_616ens_2ILEILETHRTHRLC106 - 164106 - 164
d_617ens_2GLNGLNGLUGLULC166 - 187166 - 187
d_618ens_2HISHISTHRTHRLC189 - 206189 - 206
d_11ens_3GLUGLUPROPROED1 - 2211 - 221
d_21ens_3GLUGLUPROPROGF1 - 2211 - 221
d_31ens_3GLUGLUPROPROJH1 - 2211 - 221
d_11ens_4ASNASNLYSLYSRA334 - 5278 - 201
d_21ens_4ASNASNLYSLYSXJ334 - 5278 - 201
d_31ens_4ASNASNLYSLYSYM334 - 5278 - 201

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixベクター
1given(-0.497103845276, 0.867568023171, 0.0146113716842), (-0.867270252485, -0.497316692874, 0.0227687536649), (0.0270199216514, -0.00135357301075, 0.999633978851)1.86667654536, -143.018557869, 1.09884942706
2given(-0.499987477604, -0.866008205294, 0.00650466002155), (0.865995761548, -0.500021395457, -0.00547220850893), (0.00799144665076, 0.00289697227967, 0.999963871513)-122.960214347, -73.0601988789, 0.32422103929
3given(-0.499198058352, -0.866482152087, 0.00315890047033), (0.862299372884, -0.496423646578, 0.100016771803), (-0.0850945947861, 0.0526520961813, 0.994980736852)-122.912530229, -76.3416734011, 5.15720932529
4given(-0.493678038822, 0.868677558139, 0.0410035848532), (-0.869324522576, -0.494226823437, 0.003836853425), (0.0235980599557, -0.0337512515523, 0.999151632429)1.1003910873, -142.708076741, -1.79460918503
5given(-0.501967395093, 0.864152101255, 0.0356353779428), (-0.864715962373, -0.502260497371, -0.000834983335399), (0.0171766900458, -0.0312336145422, 0.999364509397)1.02910794638, -142.957011643, -1.69350010857
6given(-0.49561539402, -0.868541679988, -0.000855180697034), (0.868464217369, -0.495583896735, 0.0129036602337), (-0.0116311805196, 0.00565255881627, 0.999916378613)-123.054855076, -72.9233105757, 0.329995915446
7given(-0.49904275397, 0.866565280204, 0.00457655495064), (-0.866577249254, -0.499038458626, -0.00211846348087), (0.00044809002848, -0.00502314224987, 0.999987283548)1.94570410777, -142.917516297, -0.024786600585
8given(-0.506817132401, -0.862004952963, 0.00915725789342), (0.861987920111, -0.506618813109, 0.0177257944186), (-0.0106404834588, 0.0168771819822, 0.99980095061)-123.080256003, -73.7577871652, 1.17592826939
9given(-0.499760098223, -0.865942137873, 0.0195973998073), (0.86210074547, -0.495099483683, 0.107975950641), (-0.0837982630107, 0.0708570046812, 0.99396032919)-123.536829936, -76.9914496136, 5.92282595184
10given(-0.486194933936, 0.873498576038, 0.0247936256779), (-0.873850312539, -0.485988029852, -0.0141868289825), (-0.000342769618643, -0.0285634819276, 0.999591921741)2.04455673018, -141.245636768, -1.28615050355

-
要素

-
抗体 , 4種, 12分子 HACLBDEGJFIK

#2: 抗体 BA.4/5-1 heavy chain


分子量: 23350.086 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 BA.4/5-1 light chain


分子量: 23390.787 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 EY6A heavy chain


分子量: 24346.273 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 EY6A light chain


分子量: 23315.855 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

-
タンパク質 / 糖 , 2種, 4分子 RXY

#1: タンパク質 Spike protein S1


分子量: 22935.734 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#6: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
詳細

研究の焦点であるリガンドがあるかN

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.64 Å3/Da / 溶媒含有率: 66.23 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1 M sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 1000

-
データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I04 / 波長: 0.9537 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2022年11月25日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9537 Å / 相対比: 1
反射解像度: 3.52→75 Å / Num. obs: 62592 / % possible obs: 99.7 % / 冗長度: 7.1 % / Biso Wilson estimate: 124.09 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.325 / Rpim(I) all: 0.132 / Net I/σ(I): 4.9
反射 シェル解像度: 3.52→3.58 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 3098 / CC1/2: 0.351 / % possible all: 98.4

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
GDA1.20.1_4487データ収集
xia2データ削減
xia2データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7QNW

7qnw


解像度: 3.52→74.69 Å / SU ML: 0.606 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 29.3554
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.266 3023 4.86 %
Rwork0.2178 59186 -
obs0.2201 62209 99.08 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 167.52 Å2
精密化ステップサイクル: LAST / 解像度: 3.52→74.69 Å
タンパク質核酸リガンド溶媒全体
原子数24078 0 14 0 24092
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002824677
X-RAY DIFFRACTIONf_angle_d0.577933592
X-RAY DIFFRACTIONf_chiral_restr0.04313761
X-RAY DIFFRACTIONf_plane_restr0.00474285
X-RAY DIFFRACTIONf_dihedral_angle_d10.84148745
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.18161673828
ens_1d_3HX-RAY DIFFRACTIONTorsion NCS0.189840607377
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.212903671975
ens_2d_3FX-RAY DIFFRACTIONTorsion NCS1.26922991974
ens_2d_4IX-RAY DIFFRACTIONTorsion NCS1.37804265325
ens_2d_5KX-RAY DIFFRACTIONTorsion NCS1.29284004948
ens_2d_6LX-RAY DIFFRACTIONTorsion NCS0.198339181382
ens_3d_2GX-RAY DIFFRACTIONTorsion NCS0.66391799371
ens_3d_3JX-RAY DIFFRACTIONTorsion NCS0.555829445209
ens_4d_2XX-RAY DIFFRACTIONTorsion NCS0.101854685636
ens_4d_3YX-RAY DIFFRACTIONTorsion NCS0.101460298407
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.52-3.570.40121290.37782517X-RAY DIFFRACTION92.91
3.57-3.630.42591270.37652618X-RAY DIFFRACTION97.79
3.63-3.70.37781420.34872681X-RAY DIFFRACTION98.91
3.7-3.760.40121310.3342736X-RAY DIFFRACTION99.31
3.76-3.830.33421430.2942652X-RAY DIFFRACTION99.43
3.83-3.910.31781280.29472669X-RAY DIFFRACTION99.33
3.91-40.30871490.27362698X-RAY DIFFRACTION99.72
4-4.090.30741310.25652696X-RAY DIFFRACTION99.54
4.09-4.190.31691490.25742688X-RAY DIFFRACTION99.58
4.19-4.310.25151430.23742651X-RAY DIFFRACTION99.54
4.31-4.430.24761380.21422684X-RAY DIFFRACTION99.58
4.43-4.580.2511340.19712713X-RAY DIFFRACTION99.65
4.58-4.740.2321320.18362745X-RAY DIFFRACTION99.69
4.74-4.930.24521480.1842679X-RAY DIFFRACTION99.72
4.93-5.150.25771390.18422712X-RAY DIFFRACTION99.86
5.15-5.430.22441250.18752715X-RAY DIFFRACTION99.79
5.43-5.770.30531410.20162725X-RAY DIFFRACTION99.79
5.77-6.210.26661200.20652728X-RAY DIFFRACTION99.82
6.21-6.840.2931380.2072707X-RAY DIFFRACTION99.82
6.84-7.820.23281410.20172740X-RAY DIFFRACTION99.9
7.82-9.850.20841510.16242732X-RAY DIFFRACTION99.83
9.85-74.690.2241440.19462700X-RAY DIFFRACTION96.5
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.795111485750.3783347646262.606516341088.08144549791-2.209024089865.702032447360.1140676992930.954209392599-0.373962372228-1.00140911532-0.4254825311840.5912537399380.620467588411.276460418360.4248849662970.9786942148640.1171385091140.01321899227211.23287486955-0.08428802283111.1410256041412.1595095343-81.744560394319.9759045508
21.14246351094-1.36550346550.07837509184622.14843166813-0.6355395913223.68868832922-0.3591902160590.921160308995-0.3666064406040.536471485093-0.0319951556988-1.171403674980.07006391005050.8470111985750.7040347063890.777897202789-0.0773869713535-0.1107305345341.587585668710.07414370346731.8013475358618.5647198883-80.128884924227.6399245979
36.227984091781.576754117852.822478026935.197360377281.077380060056.507804581660.1788732057060.02712999495380.1334491807361.35354471417-0.403128904544-0.3351908290840.3070609339880.8118673964180.1833521469640.708803930220.0326014591754-0.1275168697160.851232376522-0.008358027819950.6396774289347.66613934228-75.179863576631.2602921717
46.450568651791.80204684083.927029612971.821187786310.1975658190084.07769351535-0.02851236734690.156552068081-0.127011659816-0.449465914904-0.2010180050230.1788752697270.129232495837-0.1652357428470.08965244909790.759610995280.118870921667-0.05117399787740.926434120515-0.1032846794260.728460766938-4.89937688465-75.206531908919.6447821381
53.94649515835-0.8554614786892.620471386448.87987896233-3.445833390776.739915773070.616571852246-0.661315940249-1.117028817241.688411964270.129658401565-0.314443110570.3752569524670.39534569537-0.7317760187061.179127223440.0335252897236-0.5088387399081.337828191960.03891952147161.3119796775813.3783203607-83.309702114532.1482575636
66.51237985229-1.01056873629-1.311184046252.62285953298-0.7910331855015.674538153520.2100616168331.36567234772.11231791399-1.04437565482-0.374950073398-0.21993220847-0.21044785382-0.0277860124055-0.02496959178011.02949259944-0.0982841522719-0.06092496022361.348799708610.09849997012581.01307015368-19.0963580438-51.40203286293.18620779632
78.456409259416.81619323595-1.397123690765.7804067084-2.126891757185.49785040397-0.4141295453360.662700430145-0.979214576461-0.540492436503-0.00704342477526-2.122632710.2514185924850.09780198431650.017528374210.8825890085710.1021541182260.09305160373971.34832195115-0.09370429900570.376244348968-12.9052875073-63.55273723234.86125376493
80.803876924539-0.43946204530.760389455260.950153335368-0.4735907632321.618417804310.299307303780.2432186255880.130077695720.4917124987690.23727980058-0.0302682969676-0.914368408099-0.2425249988445.1189306887-0.08076382319150.31882977845-1.683068486681.438864510730.434611429271-2.12301642942-23.534284538-58.150116407812.3148674518
95.081433020060.2792897122510.05277121812228.12226764179-0.3440909899765.008984627330.246941573648-0.0289120037841-1.51743662757-1.999789345780.220014414182-0.8129791552320.964502856969-0.276800748823-0.02073556955271.33882615524-0.197993234055-0.1584204567761.53372637460.04212953313821.26031353977-25.3994498746-68.39839601686.51764600749
104.84812860492-1.61628724146-0.9257307110038.85062128734-0.1610961183554.02742492162-0.4814517974820.9350003963350.625884593964-0.8279001236310.191025322843-0.3239097698260.207221918176-0.5907467792880.02016301377630.7194483090820.0628054809461-0.1602860924231.13998355050.01409722325340.503640109714-21.1394133406-57.78240104586.53819996137
113.733167223930.9026515755450.8231781979445.249234559112.866532695986.17530641590.1882611295260.5092373903941.44767433016-1.30069026283-0.0266285768105-0.524256165158-2.006954400380.528361432032-0.06675591777811.279620217160.1465710659160.3574233851271.086326632740.3537134099261.86576278039-22.8391712776-25.576922867913.7892158111
123.29726345729-0.3487859317852.126225378765.229700637911.334934190676.30475508257-0.07295640980260.2012068998521.1880404653-1.115914237580.339965088063-0.0669539292052-0.5675960555720.590758822417-0.1493530492581.14324454224-0.1844516813130.09424349671331.403721227160.07722828021281.648253177-19.6295050387-21.936977905317.2021314607
133.189518164430.681974246403-3.036888589315.45495037-0.5764642241022.91635584937-0.884901161031-0.47450515349-0.01371922886860.64186509610.9256058006930.700699142589-0.3013531101550.1541856529460.4620908685690.8898175747750.113823238222-0.03708505972461.46102334842-0.01713618928440.748751033302-23.1361874088-54.581837039933.4390821729
147.06508324222.11835509559-0.5941389288944.473587788931.767572238364.28785560509-0.520074687292-0.180418282638-0.1165484879160.232683354776-0.03388546789441.374857859780.967706138412-0.7561810480750.4475010026990.891302587798-0.00068515035732-0.2079535624671.30909373380.09004121683940.625018315155-22.8841487572-62.996597269628.9735916105
157.93559181535-0.3582426366093.148885576123.917178639171.149679680481.836476991170.0369168455734-0.627733459119-1.610728877961.02720753158-0.117175942558-0.544112555503-1.12084492058-0.0297341692681-0.313582206381.026473789730.146073126763-0.3215401301911.30613619466-0.12449452160.41880315644-14.3991175813-61.923369528728.8334014066
162.07990283727-2.22188999071-0.5975257855525.189902264312.468404105413.05498709476-0.125583981217-0.692043257256-0.4639257615250.0550515040642-0.5875825771260.2010919144650.130551540556-0.5255259889440.2572361287980.7921988934250.03056109474360.02027065436381.263953957260.00831541758810.914693785749-20.2965712884-58.567931922225.9597497104
171.68501867478-2.09603659934-1.74432791345.716662477713.075432559912.04223627576-0.12534718921-0.557871755875-0.0408628158591.284881984381.15830239171-0.843394124591-0.2744086208860.702515749642-0.446915431121.110251956960.184582494384-0.2085820492261.34746881272-0.3242149365521.29340622411-18.9497603105-39.182872725737.4859643
183.90042785014-3.36326571176-0.1349749533574.722363027381.453614871884.260858521350.7273542398850.6123043159840.839413052832-1.06608471758-0.376632495607-0.1671269656670.2968034290550.136380009858-0.1148241074860.968531736981-0.04685543758630.2579031309611.140442962120.1617725880031.46606902082-28.8794666148-24.964000676624.2392089818
197.17983886409-1.949294036510.5880474914681.874202431551.575288263773.486585415480.36518838196-0.5681763777720.3615578774770.996859718587-0.608071602237-0.151425143098-0.546230381206-0.5777006675130.2136294763510.8196210079350.003163133805820.03462223855931.244796987980.09553337091111.43272946079-41.1418649868-27.986634501628.8952080192
208.2804991488-2.533875077522.783229011693.39455152910.8926567724354.83873983328-0.5546210009120.3583239323370.785331678959-0.5431552567360.629180198498-1.01283146147-0.1941356668930.651423778528-0.1343182102181.117146902290.04610106569370.3215083977931.30258778904-0.1303137313331.48393890113-22.6140761869-34.76995951127.3896661996
215.40426214975-1.927679235642.144091970373.53146706351-0.2290001136436.40862747049-0.017315793532-0.5095564098670.944650101130.361115432890.155431632017-0.0369133064899-0.354852695585-1.18414560430.2163529562471.047927437260.05046443234650.05478593342781.1069336929-0.05421032018951.75256252178-36.9724453596-23.242867594527.3841219748
225.351675002361.00379090067-0.2694281368232.04762522714-0.1621123453883.881610781470.564237358205-0.347243363610.4234684874020.359206954514-0.256264512631-0.59455604419-0.3346481893890.302930830546-0.3658047771810.826911113006-0.104212904951-0.06693290562641.152703768550.03323315546831.1677503255423.3032326178-58.357027384243.0206232123
231.513776171050.183414048109-3.542548848442.038515165740.1072554079859.646034293841.35739876831-1.138899942760.999160796474-0.492479723232-0.0867066808251-0.459657809326-5.048121292663.33590552396-0.3345858042812.17376783955-0.1485442406770.3970151434271.41227548942-0.3014599747892.2078433399115.9402413676-28.446842590354.4438299087
241.955138621230.494827001516-0.103933354212.476488342162.159940090652.035018663060.631431890626-0.9084227828171.29751751697-0.8684727025240.06827259305210.247662525907-2.545034929390.481958410536-0.6638853229162.43578694329-0.3477806716130.2025485190191.85652734577-0.6126696878612.0643679617913.4375525801-29.609026134462.7077032837
253.248907747561.489648729833.246511367466.43723273673-2.557262906346.05294440484-1.28112489254-0.3563455063552.480103018181.84761042471-1.77298808414-0.299801710747-1.62208419275-0.2448554163872.671606850712.76778121285-0.452692520916-0.1663851042961.91795221567-0.3872905111862.4562007675422.3437782313-25.347526441159.005688891
262.311719916230.1608142508631.668542990042.787276543061.155644319093.53463548250.614013524984-1.605875455930.311245495540.5535366008930.1312198100910.3346445597470.462534034084-0.485352557366-0.5069430553651.63629909911-0.29052708610.1346536240621.96394793762-0.145108522220.9967240548511.5090786333-59.705009442858.2071717285
271.824650910450.4890589814650.183994206562.453574619891.204722615260.5380333723571.05924396596-1.534901602890.69875014431.27798051757-0.9991667131930.6454835313160.1004288762250.0107377571066-0.02021601006481.38534782012-0.5826656298450.0226613901911.85235383071-0.03088000504580.60878306161610.2486817054-65.953268498956.3956559837
281.60820414422-0.11036817921-0.455422848252.39699770207-0.8893879970134.598836116460.7951254593-1.197191260.3487740495521.10749668461-0.5315297347740.1781104609491.08804114966-1.287569723010.1067718477731.4093592681-0.515378738649-0.2349516447421.75315268535-0.158638351010.8646334854987.43354072406-64.360040614856.0320978316
291.91420865672-1.53639862924-2.022623621161.251792868711.571642002213.773462542911.06230841627-0.5604703929050.56856352602-0.141802693114-1.033614085480.1897886922120.477938086648-1.39228377153-0.06684468588051.55130870238-0.3024567933030.1461146308482.22638562461-0.6139735963662.003059587680.40279965408-46.60834624868.381549981
300.317546451880.370325627722-0.1881897692013.05590563235-2.290761252561.711205821751.44045414009-0.305189467231-0.0585773135442-1.96693333407-0.7169838304091.70309944654-3.227279053750.684316523048-0.9353358836223.91574617978-0.01214496630270.3604334417632.40371463303-0.957678863212.547105061126.95688564866-19.620335001856.4063551905
311.786708310940.38418484091-0.3151832074273.059260192883.036037890273.27089105741-0.2332521147930.2809801459831.567535203080.195666348021-0.06185506849090.269704432101-1.36282867523-2.36055277232-0.3338984148261.502126104420.554592971537-0.2770959115352.30912273489-0.6497669464422.20234087661-2.8334461247-31.053552402956.1060036096
323.847830423971.165646798830.8526421170596.517807269060.3144203107245.39159072049-0.838572693259-0.7197114157150.61724672951-0.560948821715-1.34174943791-0.359685538536-2.62184971043-0.1601762977610.963096518951.93290970950.4533495982910.2206111985052.69084971364-0.6817007827141.81619022534.86890277761-36.215710942159.4232797929
332.063610356190.5040231140830.146193939662.69563212028-0.127963271952.157409638870.0385412477358-0.9406952799981.07007814367-1.757084463141.112814661310.727522404048-0.683219240981.72969184507-0.9804536044841.981661584010.3860546569360.2714810964622.19366421118-0.1947370367272.44136708278-4.19075503222-21.286285335652.3292039635
340.0945349297120.511643629936-0.3546358046016.0657048057-1.876393813740.8784795600851.411328084710.2180398662991.70371567439-0.612637528111-0.7875335972661.00107235057-0.9569450355250.116838323131-0.9640079369161.950335168750.3263505570110.2077046068412.40655440531-0.1001464061982.65325867453-6.78922568521-25.581156146162.8727828859
354.26161820868-1.71332269033-1.705370758683.484937361970.001900848074862.85784915257-0.422165831012-1.46553150049-0.4625277855640.3365052559720.7696811555980.5793286527610.416541808918-0.0434044588161-0.3791098760750.9427114553460.251913059841-0.1155807025951.487678583120.2506763515161.21660569583-83.6966804374-22.604271947242.9765281442
360.278491435588-0.1831103573940.0613377604530.749278673513-1.264834983571.99604680968-0.462481746863-0.8388664817150.003369707662080.3129540949431.68768428266-0.2108155361642.27819105204-7.98887632519-1.284987871012.00810870135-0.721487577083-0.2515484006463.230375876370.728833365592.18108790267-105.559721587-42.523905154356.3774212211
378.575052896043.40653092347-2.147564317364.489721945850.7354609379691.213254101290.767659972172-0.8581000993260.6164286433460.530653813425-0.4532616537470.820207561035-0.932805160075-2.909706601450.4888266930691.90009120944-0.108872056301-0.05844311477923.425128544360.5598572485222.10406892534-106.413682893-41.001912676863.0515203335
382.24056154533-1.773546972630.4263645101541.31089100546-0.1980665300681.81835648141-0.161554306682-0.77808590466-0.7041364436520.7745491187240.5955220920190.1707863012071.013397759910.148580310701-0.5308420038351.443365656620.5260942782720.1257269981092.107174777370.3403114163561.18692223704-71.6105017034-33.713393941358.1407822237
391.56480458533-0.5058827211330.148936872320.5779534703760.5315365658290.1973496312590.4491193272781.17800976034-1.038482418070.722823752010.7896535290120.1723281611181.36743428121-1.22493156074-0.3926626079882.4856624633-0.239309030469-0.2283383052143.246997596490.9049677504932.68303016858-97.6629450238-56.171592361861.2356453412
401.64239787081-0.270750138929-0.2603638280173.51338103176-1.962913297464.350363831350.358282875528-0.0491417381497-0.2117511774712.958132950290.1744792596851.64566932078-0.320292992813-0.010537380381-0.4451158752922.17987155713-0.1952117519150.7198733579621.166401875490.01895936662171.65883494208-60.4646181229-133.41058297742.858351077
412.567038569952.237107117074.428735302642.199407490964.027380179267.135511428190.272153748551-0.285032803148-1.227775721171.768808762131.00538148350.310777062316-0.05954796359751.00567043453-1.386709823332.61635239248-0.3071054215570.1486410460251.539748384950.2830060397691.13649431067-40.4639257575-138.41162457151.1342379202
422.29558747451-0.975957399229-1.103243764330.3789779884810.4428286433730.4755045705591.17977107228-1.33765897961-0.9547384086361.00443517719-0.978263587759-1.137859625920.5752959947610.7913354408080.404809412583.228228256390.103844040233-0.62408376192.932314196120.01337890184271.55076939697-29.276396219-142.63620547259.663123239
431.91434174496-0.39708093293-0.3556999086890.04591960372420.1358650406320.3361491683150.609646928211-1.60957543001-0.8714568328432.38616527447-1.00418730454-0.5430149434040.350008402047-0.717474175469-0.2172062046723.88795405796-0.636531630672-0.008055499840351.979112119830.2957572419861.1868020351-49.5826576757-114.16672545458.5425632786
441.62384813812-1.00439584618-1.302860861051.78892343753-0.1551568675381.685664838640.758453030829-1.328734087320.6757922780452.69776497419-0.1173673351350.691709461043-1.382718609191.05145222141-0.5654186859054.5973907369-0.4856079598480.8181402924591.66750712624-0.2396263531.56611940323-59.4421912275-118.39665037256.9821879027
450.566640263958-0.523693308772-0.4866135359080.9306097904761.009913929411.34959375932-0.207180808194-0.7520143910430.0451694372451.322879026780.336472823816-0.734898396622-1.285893533011.6778594878-0.01241030749684.15114538743-0.242228512650.4969002370652.10887607762-0.0992664152491.40229837762-52.5682881917-117.43988558659.0835607978
460.966348865131-0.282711666331-0.4862319546710.3501870997951.074296321853.01319255772-1.6055367882-2.15015656590.9244572071091.752912665540.216260195903-0.04721709799770.390127058786-0.1873313499020.6718697453973.833590401590.258473302405-0.9478200794824.01842869498-0.9969933808682.25749086389-19.7035161293-134.85857923957.0262428235
474.602137684630.864133282664-3.197993581894.762597595590.7166216787072.705109409940.5469351107522.23137326256-0.8854475131383.23073017474-0.646349176149-1.397238360680.0501503977998-1.66486054136-0.03586767800622.82907549239-0.142570215699-0.4880670387153.44670874798-0.3701985966842.09275561042-22.7830794246-125.8323402855.3677270365
482.38764475289-2.616636612450.6078583382834.04412897718-0.9152004100480.1898219781090.221250305836-1.354048871270.2626829206930.6720816186270.3581360697130.280508032233-0.317813227771-0.3760198912680.7516636825392.411072462510.250234794625-0.3562713693333.22961999839-0.2212256670883.16032438622-16.0391046565-125.11564160664.4494105352
497.06556447318-1.9103026417-0.7174899095595.141352100110.3118533094522.106780801680.2583516398620.0441728997437-0.1454733032890.301628001968-0.8324566302681.92061962965-0.142504689159-0.5023870548650.2339057204871.17894826788-0.1639099419560.3542375889081.19994050342-0.001261918007822.28226455897-75.2738047905-112.00506505521.0477245296
501.552555411870.008652929209230.3560610417650.0487639849359-0.09414446158390.358789166539-0.227149311207-0.287803196173-0.1090551211070.385028985081-0.3646746558382.299064232140.6660106391930.117336591005-0.516196466591.51815838415-0.09039654760240.6443537048351.22455889357-0.09857738117713.08029019536-76.7863164959-118.31549758528.7586361007
512.07947630350.3714917764832.24007600564.44646382817-0.3439311038532.52455275129-0.24695645208-1.116039293560.5260055503291.769218327140.1138640533231.707659494640.317127342262-0.210123301013-0.6020529902721.21800423594-0.04234745395910.5807402603771.12178909272-0.1569705891471.7173868009-66.9347303731-111.39827171332.0431707793
522.74166366407-0.567013782034-1.504577316023.58513614317-0.1654333439494.07230058870.0615695690130.2583242947110.3501134976880.611451238858-0.4526670435861.59902839071-0.0202140385904-0.1300929491170.03007453081390.958887968122-0.1465689177460.06202640257851.14036028969-0.04350428110891.85983084225-62.0584403386-98.65023150321.1794796422
535.87690199477-1.49658253715-2.108456573063.91650891382-1.314109921272.35138579259-0.2135577015710.457602091483-0.1072613803420.0132512043724-0.3285145677121.641844299280.773930363719-0.1411094907880.04415504794981.38198503285-0.2134515956380.2392137548161.15371604269-0.1703759564371.68067283052-61.7894513747-112.4604618320.3889985191
548.722741625141.572840231540.5156681540764.45625208574-3.538943088453.19328839511-0.962464114984-1.36167126742-0.6068163954071.473858441670.2848757011132.56482998028-0.1514830599870.8280540484180.4269644370271.98824100247-0.04282838624461.129240781031.869347617690.1998220178682.94450401196-84.983440503-111.87715116940.0479420778
558.95646809254-1.935847514211.788545149165.467257863740.5662070209462.674635034340.2310115456621.25050561632-1.337247606930.20936611062-0.387545680895-0.598672609357-0.04129756300120.7913746849821.225517492951.02466705546-0.0712163775728-0.1197927715141.28531397564-0.02851168677330.388715571108-33.5197961184-100.2898825343.36404661565
561.84441441063-0.247845257867-1.03890474226.50691682005-0.8292620820030.7505688157891.008855370850.08245052172940.0197967191257-1.37864001621-0.1406409682642.17338782559-0.3372691073690.1946271622431.139773997330.916520371735-0.308443767541-0.4600073797321.36035258956-0.03561340719580.755634713519-47.1583339341-99.46013489565.18263555036
572.31447342105-0.8551660473780.2089171025253.675450746331.413189210670.664507296540.2003417072030.4975466345950.6205251022870.6366476724190.5522382293860.119236402040.3858445997290.891189413940.1570043508221.00459983976-0.2769196544730.02123704155451.137177269340.07729985164031.14027602059-37.0370522477-93.084303215912.5630130535
586.06313308076-0.63201498753-1.513332150063.714831077110.4721175042060.3858961105821.605550831091.987306956770.137863685144-0.247228889063-0.06017641158630.0370166224087-0.634489297089-0.1350475270330.7919843838221.48834722942-0.125524662899-0.2118149723821.562243966780.1252056051042.09931970507-44.9650258273-86.28339662356.83540409988
596.33078740168-0.417980235771.438792408253.06958012775-0.2114725267542.03459992569-0.4322556441850.69970056871-0.0326048037026-0.869491064866-0.01783439750040.3760651312030.2580904631740.5931477320890.4792846445980.937607399385-0.136267090032-0.07132549446771.098612653970.05120309767280.857400540657-37.9746515322-95.32953454456.73534820219
604.44883540914-2.90624745677-0.6701055442654.33372244519-0.4984298936631.304230358780.1125692104740.433461074741-0.756813569437-0.7473131501860.0503825942653-0.9342374225551.405896884240.4864228388910.09498907602261.075972435890.000642256087429-0.05395374508681.21339504155-0.2200788804841.4795632458-8.99237144911-109.99875097813.8511204596
611.525206927141.0516705436-0.9730205720823.53239538729-0.134159408173.59750740130.5677101985010.467551725325-0.572111947040.433374537842-0.430193599029-0.928674689630.2978448153920.3000351156960.1017711336411.402033576190.0945646152788-0.09463554871381.18179887074-0.01914975839391.70565882189-7.383052918-114.60951860517.2740795636
625.56126398338-1.49007606822.04059433862.769265300431.584339480432.661022855380.203677272289-0.0787565036569-0.1350778854151.13758948615-0.828522431579-0.207046316959-0.1870806496460.676505405571-0.2512249454861.22852779614-0.1593799186860.009278795692371.16286823909-0.1830452301280.441015239158-33.8452794623-95.25167539733.6161700539
632.65985540785-0.02689959688792.031605749793.84700314839-0.9767557623711.7719901887-0.0563924239334-0.1278709045580.6585621730691.24958875249-0.9821889435860.11635699875-0.2647328699540.346198049526-0.6224176696431.1670298681-0.09904371088880.03062133345271.064621025980.04623998606530.881070440827-41.3177389078-91.21083692529.2499938811
644.445379103081.935383500320.1629688069447.80275371971-1.73794672271.70216189001-0.0533143209125-0.52921726342-0.05317171594810.5492361667320.1573098613341.243988801220.395032177580.54251692813-0.1625445590111.05473057518-0.2368292884530.1138475189551.277347999720.03337591863560.676699723378-44.6236474965-99.154952017629.1156419032
654.02699954811-1.240827085071.499046135084.92699481857-2.375867170073.61363310918-0.232130291489-0.3817249885650.198943833380.7590126071890.1799920783220.871569738325-0.5143992132350.0763373820435-0.1692490201111.01203825123-0.1595076048640.1469639724431.12379478505-0.1882387682840.966228723381-38.8755770392-95.737597248926.2363901857
662.8213935619-0.2180950393472.393359211093.27984933455-1.019510689822.11723595717-0.447405050430.201211523744-0.6406829256550.1154879812750.796153445613-0.5488802441770.837395484052-0.1128784327380.9125157915330.955567587098-0.0904174851833-0.03038444354481.02619196161-0.1867692239851.42602787047-8.70956697872-106.35617583226.8450860812
675.600947807891.61375153978-2.462293658521.27167906553-0.2964752506512.696128023170.1934727284110.4294231135020.07217973701290.5106785932330.1157588789960.130196684644-0.455420225466-0.4557199046340.009804711858571.140167650440.125981310755-0.1949391216741.083561308860.04261767777231.45255352423-7.43760490725-99.314116601229.0153383874
685.477429834952.45523266363-1.722590484584.09198284548-2.556752978651.910433011680.1086731479480.0269997575316-1.047429272870.0306437230585-0.0187447380456-0.05515270024770.903967897572-0.0722286207544-0.03007285976681.506248758340.00414785335245-0.3057953051631.27878387893-0.05012216343961.21052189449-16.9990771689-105.65217075427.5172990389
695.385881343041.524300398030.5092365351513.77840256251-1.425814167393.39806840902-0.4022928489040.0243382997778-0.5389759155890.2363300514230.376082095457-0.789770909630.648166630020.6149818661590.2387509902651.061732325350.165054472369-0.2088134987041.07874805679-0.0516769715321.504973869330.0991198785741-98.898221328127.4603086761
708.598532253230.008917739330150.7604384729395.55346008230.5484234434954.04109809466-0.0569165711770.685404729881-0.0668797310989-1.290826282630.833735920423-1.17721227978-0.5904960470760.00500763882308-0.7531151715131.120373354110.02030774567930.1036353709371.395577095210.2029223319531.0643915767-57.8940123173-21.141579327219.7330608114
710.4184046985590.5799296110690.1693391177391.05771886680.5631886946850.4531927905770.6870459433520.1504977290051.35295072499-0.430430092009-0.9810699866920.650525105528-0.409181060613-0.791595703042-0.2716083212031.19123611660.312552088582-0.184901691981.63166960837-0.01095271717722.01590866007-62.4199455264-16.286780650927.3008846688
724.76605870091-2.760885553690.9417595516411.63155760651-1.09305116643.22903436404-0.77292602607-1.387121735190.08841406228020.7889101089550.7288008203890.109358035729-0.4468843164-0.2542901961670.3783171288940.9499527834960.1125459054160.0302687618861.282217954640.008701309806830.749463925649-61.3081859493-28.154660949631.0776859514
733.26014189197-0.460480620099-0.8932567969281.762776574231.645164839132.67550514781-0.2599150196820.342624581707-0.310818264994-0.137338491720.05983132026070.06261794651060.177722166507-0.0544069967486-0.288987269390.8181604631110.103339706352-0.07124827086621.090352909760.06844044833740.969561015779-55.0536128775-39.21376227819.5994613851
748.875544844650.9433628579451.439443774276.37394581298-2.218463314681.2050579436-0.434854889395-1.618507309730.892916340680.3534889432290.13888935776-0.420276372336-0.888278200530.04728324249881.478911494750.8819121450370.1856972204840.09014510405681.40228685849-0.1558840028330.967231950583-57.098992503-19.160633733431.878272237
758.060876129411.704403791183.00431007195.2504986357-0.6843826201823.094920554530.09906979165850.676543719998-0.614259528111-1.40498546263-0.7533063398932.752922524141.425355579810.565411736298-0.4269560655811.213901251680.372773845663-0.251154069831.62090950486-0.06822438570950.973520409059-68.6415488509-63.65460086183.65196348168
768.374625510673.028930051363.499548096983.214350629572.001403236762.32065815835-0.07641706749671.067634966141.93070134561-1.10925091675-0.4823611608310.40122053331-0.5543138162470.189353348416-0.1794490740081.31303568950.135289702703-0.300227203221.272692455080.1593927364131.11602430517-61.2596847561-52.18458187985.13289436658
773.787295162070.282917841732-1.389553234994.24136251141-0.9685510663681.777846955220.348148110264-0.215639356153-0.336383282533-1.491414752220.0698253929461.269780061161.28687555705-0.45105953152-0.04490780438931.124757170340.15624293915-0.02341356510920.985921317213-0.04235151479021.06840416436-60.598214817-63.924050847112.775923263
784.73615772504-1.28387300595-1.600993497410.893145969160.866855984340.897498891691-0.5812430650440.7886670518260.180714841916-0.4443735975441.98633711667-0.176471941424-0.4573349484141.19171156433-0.6977991391061.928834915340.290636467342-0.1954080655691.541260890550.04544273424391.99646240767-50.8115664461-60.51663017116.88705041592
792.945276992520.6407330815070.3360881089686.027681872470.9374638485080.6603757821340.3665964659620.7816155680560.3506692337-1.1059147743-0.316019537780.8390303454250.4456859435940.0549393720892-0.4998329695911.185272115550.168255118291-0.1309080014761.1756062526-0.179985624051.28290951395-62.1103640238-62.14445123196.96067452912
804.864594426220.94941818385-2.335198935051.48870291477-0.8304747583063.73917826190.2378528142260.0448919295589-0.892962569641-0.672250459923-0.3783225483651.399828758050.309466520733-0.786116822567-0.1399285273141.14034331885-0.0906254619794-0.3044491904361.3693484461-0.1867492091742.84988696895-89.1195245257-79.691549294614.8715011044
813.83114658814-0.3188698405910.4097233502832.812724653551.002269318352.780224218380.03609745558260.1430044663330.1466766120570.0584742558050.6846163895620.711474272168-0.432570645271-0.091684448044-0.1510841858140.9809827647790.007683919559260.004675826413591.61786556011-0.1505955425122.515510815-93.8926997577-78.717647910418.3493490174
823.722250240622.290059479810.7326246093812.7462521443-0.9739309139881.57476227049-0.367951469147-0.769535536249-0.3413205546721.191941931920.263094816947-0.265198560219-0.0536152417010.06828400050020.6988340740651.384782745970.230605623365-0.05583581804251.195847831170.005653063934771.13204311659-63.8696743262-65.077750164133.879585766
836.97749018601-1.64615156984-2.349405401365.052776094841.014133020822.04837436254-0.862486118574-0.2484106468190.6714074245870.3535124888290.27960217169-0.6356566630660.9478884700310.6552890307620.1004855675751.228483702620.1626779817850.01810936447251.11537511869-0.02407194904710.986677382471-56.7128167036-60.685373761129.3451086215
845.07424378635-1.87858331718-2.397447488946.90288529308-1.214255302433.037098127740.255588758925-0.7072759430110.3409192941060.796711311710.06235651370560.416626477606-0.189385609531-0.810678336850.6949078961661.024199697770.1268651424460.1093276280611.112965934120.02873548416290.981685867577-61.9257974986-53.937231231129.0777036885
853.620842615820.4702431488210.07270505661083.376478641971.518871819882.18652113698-1.03196023877-0.465386832767-0.9359362289870.5270748357210.6172533606650.05054680426630.8894980802880.05111702324860.157554354290.9326479831930.214604313313-0.02348420702311.131924583140.1511227349181.59957866344-61.8625094987-60.724415407326.3227411318
860.76677429691-0.202422524540.4630015667172.89921461533-1.6788055881.099546874030.192870955855-0.0527562228522-0.4340838648150.304839554636-0.04267138493741.25411539280.7974900467550.01386768356480.2728436134990.991481239002-0.005611150497430.3260140433681.34721537438-0.1512212537732.11043621005-85.9037525413-81.510225068227.7813396796
871.677299268321.32769414481.511215018044.763363927180.9359031121242.33382486203-0.1605017592710.147270245655-1.14782579333-0.7018696823490.4731544948470.7842151867090.1471958594430.8245165625130.1072619003520.991509983482-0.1079450211710.03783524857471.381396415830.0347402807862.35440227349-80.3503837246-86.030981964929.9540105685
882.73323824105-0.3990219003570.928034298137.349229470632.930967418661.766072627690.1030242103620.09896560795670.0271154684258-1.00381469744-0.4513500684830.087575569954-0.9171776952480.04846151557960.4329749309771.47596667933-0.0948113356510.5877543820761.43174002931-0.0149314440132.18667181768-81.1694489088-74.627501099128.3195005335
892.08714031939-1.34722114670.9751017409363.561004107991.518445535244.41730125220.007172515426890.0968884639394-0.01518682168160.863252966434-0.2243971927441.741049981941.53513016227-0.2875526255520.1831305076831.13474202747-0.2365565923060.3764477878051.4118192353-0.05198125165782.47175861444-83.7208532708-92.834237307428.5311496538
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'R' and (resid 334 through 353 )RA334 - 3531 - 20
22chain 'R' and (resid 354 through 375 )RA354 - 37521 - 42
33chain 'R' and (resid 376 through 421 )RA376 - 42143 - 88
44chain 'R' and (resid 422 through 506 )RA422 - 50689 - 173
55chain 'R' and (resid 507 through 527 )RA507 - 527174 - 194
66chain 'H' and (resid 1 through 17 )HB1 - 171 - 17
77chain 'H' and (resid 18 through 34 )HB18 - 3418 - 34
88chain 'H' and (resid 35 through 53 )HB35 - 5335 - 53
99chain 'H' and (resid 54 through 65 )HB54 - 6554 - 65
1010chain 'H' and (resid 66 through 113 )HB66 - 11366 - 113
1111chain 'H' and (resid 114 through 161 )HB114 - 161114 - 157
1212chain 'H' and (resid 162 through 220 )HB162 - 220158 - 216
1313chain 'L' and (resid 1 through 18 )LC1 - 181 - 18
1414chain 'L' and (resid 19 through 38 )LC19 - 3819 - 38
1515chain 'L' and (resid 39 through 75 )LC39 - 7539 - 75
1616chain 'L' and (resid 76 through 102 )LC76 - 10276 - 102
1717chain 'L' and (resid 103 through 113 )LC103 - 113103 - 113
1818chain 'L' and (resid 114 through 144 )LC114 - 144114 - 144
1919chain 'L' and (resid 145 through 155 )LC145 - 155145 - 155
2020chain 'L' and (resid 156 through 174 )LC156 - 174156 - 174
2121chain 'L' and (resid 175 through 213 )LC175 - 213175 - 213
2222chain 'E' and (resid 1 through 119 )ED1 - 1191 - 119
2323chain 'E' and (resid 120 through 162 )ED120 - 162120 - 155
2424chain 'E' and (resid 163 through 201 )ED163 - 201156 - 194
2525chain 'E' and (resid 202 through 221 )ED202 - 221195 - 214
2626chain 'F' and (resid 1 through 18 )FE1 - 181 - 18
2727chain 'F' and (resid 19 through 61 )FE19 - 6119 - 61
2828chain 'F' and (resid 62 through 103 )FE62 - 10362 - 103
2929chain 'F' and (resid 104 through 114 )FE104 - 114104 - 114
3030chain 'F' and (resid 115 through 129 )FE115 - 129115 - 129
3131chain 'F' and (resid 130 through 159 )FE130 - 159130 - 159
3232chain 'F' and (resid 160 through 183 )FE160 - 183160 - 183
3333chain 'F' and (resid 184 through 199 )FE184 - 199184 - 199
3434chain 'F' and (resid 200 through 212 )FE200 - 212200 - 212
3535chain 'G' and (resid 1 through 119 )GF1 - 1191 - 119
3636chain 'G' and (resid 120 through 162 )GF120 - 162120 - 155
3737chain 'G' and (resid 163 through 221 )GF163 - 221156 - 214
3838chain 'I' and (resid 1 through 114 )IG1 - 1141 - 114
3939chain 'I' and (resid 115 through 212 )IG115 - 212115 - 212
4040chain 'J' and (resid 1 through 107 )JH1 - 1071 - 107
4141chain 'J' and (resid 108 through 143 )JH108 - 143108 - 136
4242chain 'J' and (resid 144 through 221 )JH144 - 221137 - 214
4343chain 'K' and (resid 1 through 18 )KI1 - 181 - 18
4444chain 'K' and (resid 19 through 61 )KI19 - 6119 - 61
4545chain 'K' and (resid 62 through 114 )KI62 - 11462 - 114
4646chain 'K' and (resid 115 through 140 )KI115 - 140115 - 140
4747chain 'K' and (resid 141 through 199 )KI141 - 199141 - 199
4848chain 'K' and (resid 200 through 212 )KI200 - 212200 - 212
4949chain 'X' and (resid 334 through 353 )XJ334 - 3531 - 20
5050chain 'X' and (resid 354 through 375 )XJ354 - 37521 - 42
5151chain 'X' and (resid 376 through 421 )XJ376 - 42143 - 88
5252chain 'X' and (resid 422 through 494 )XJ422 - 49489 - 161
5353chain 'X' and (resid 495 through 516 )XJ495 - 516162 - 183
5454chain 'X' and (resid 517 through 527 )XJ517 - 527184 - 194
5555chain 'A' and (resid 1 through 17 )AK1 - 171 - 17
5656chain 'A' and (resid 18 through 34 )AK18 - 3418 - 34
5757chain 'A' and (resid 35 through 53 )AK35 - 5335 - 53
5858chain 'A' and (resid 54 through 65 )AK54 - 6554 - 65
5959chain 'A' and (resid 66 through 113 )AK66 - 11366 - 113
6060chain 'A' and (resid 114 through 161 )AK114 - 161114 - 157
6161chain 'A' and (resid 162 through 220 )AK162 - 220158 - 216
6262chain 'B' and (resid 1 through 18 )BL1 - 181 - 18
6363chain 'B' and (resid 19 through 38 )BL19 - 3819 - 38
6464chain 'B' and (resid 39 through 75 )BL39 - 7539 - 75
6565chain 'B' and (resid 76 through 102 )BL76 - 10276 - 102
6666chain 'B' and (resid 103 through 128 )BL103 - 128103 - 128
6767chain 'B' and (resid 129 through 155 )BL129 - 155129 - 155
6868chain 'B' and (resid 156 through 174 )BL156 - 174156 - 174
6969chain 'B' and (resid 175 through 213 )BL175 - 213175 - 213
7070chain 'Y' and (resid 334 through 353 )YM334 - 3531 - 20
7171chain 'Y' and (resid 354 through 375 )YM354 - 37521 - 42
7272chain 'Y' and (resid 376 through 421 )YM376 - 42143 - 88
7373chain 'Y' and (resid 422 through 506 )YM422 - 50689 - 173
7474chain 'Y' and (resid 507 through 527 )YM507 - 527174 - 194
7575chain 'C' and (resid 1 through 17 )CN1 - 171 - 17
7676chain 'C' and (resid 18 through 34 )CN18 - 3418 - 34
7777chain 'C' and (resid 35 through 53 )CN35 - 5335 - 53
7878chain 'C' and (resid 54 through 65 )CN54 - 6554 - 65
7979chain 'C' and (resid 66 through 113 )CN66 - 11366 - 113
8080chain 'C' and (resid 114 through 161 )CN114 - 161114 - 157
8181chain 'C' and (resid 162 through 220 )CN162 - 220158 - 216
8282chain 'D' and (resid 1 through 18 )DO1 - 181 - 18
8383chain 'D' and (resid 19 through 38 )DO19 - 3819 - 38
8484chain 'D' and (resid 39 through 75 )DO39 - 7539 - 75
8585chain 'D' and (resid 76 through 102 )DO76 - 10276 - 102
8686chain 'D' and (resid 103 through 128 )DO103 - 128103 - 128
8787chain 'D' and (resid 129 through 155 )DO129 - 155129 - 155
8888chain 'D' and (resid 156 through 174 )DO156 - 174156 - 174
8989chain 'D' and (resid 175 through 213 )DO175 - 213175 - 213

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る