[日本語] English
万見
- PDB-8sja: Ara H 6 13D9 16A8 -

+
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: 8sja
タイトルAra H 6 13D9 16A8
要素
  • 13D9 heavy chain
  • 13D9 light chain
  • 16A8 heavy chain
  • 16A8 light chain
  • Conglutin
キーワードIMMUNE SYSTEM / allergy / peanut / antibody
機能・相同性Napin/ 2S seed storage protein/Conglutin / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / nutrient reservoir activity / IgE binding / ACETATE ION / Conglutin
機能・相同性情報
生物種Homo sapiens (ヒト)
Arachis hypogaea (トウジンマメ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.68 Å
データ登録者Spiller, B.W. / Shrem, R.A.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)5R01AI155668 米国
引用ジャーナル: J.Allergy Clin.Immunol. / 年: 2025
タイトル: Structural determinants of peanut induced anaphylaxis.
著者: Smith, S.A. / Shrem, R.A. / Lanca, B.B.C. / Zhang, J. / Wong, J.J.W. / Croote, D. / Peebles Jr., R.S. / Spiller, B.W.
履歴
登録2023年4月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年12月25日Provider: repository / タイプ: Initial release
改定 1.12025年1月29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_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
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
L: 16A8 light chain
H: 16A8 heavy chain
B: 16A8 heavy chain
G: Conglutin
I: Conglutin
C: 13D9 light chain
D: 13D9 heavy chain
E: 13D9 light chain
F: 13D9 heavy chain
A: 16A8 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)216,57512
ポリマ－216,45710
非ポリマー1182
水2,684149
1
L: 16A8 light chain
H: 16A8 heavy chain
G: Conglutin
C: 13D9 light chain
D: 13D9 heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)108,2886
ポリマ－108,2295
非ポリマー591
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: 16A8 heavy chain
I: Conglutin
E: 13D9 light chain
F: 13D9 heavy chain
A: 16A8 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)108,2886
ポリマ－108,2295
非ポリマー591
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)108.466, 112.067, 223.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 2 through 214 or (resid 301 and (name C or name O or name CH3 or name OXT))))
d_2ens_1(chain "L" and (resid 2 through 214 or (resid 301 and (name C or name O or name CH3 or name OXT))))
d_1ens_2(chain "B" and resid 1 through 221)
d_2ens_2(chain "H" and (resid 1 through 136 or resid 143 through 199 or resid 202 through 221))
d_1ens_3chain "C"
d_2ens_3(chain "E" and resid 2 through 207)
d_1ens_4chain "D"
d_2ens_4(chain "F" and (resid 1 through 135 or resid 142...
d_1ens_5(chain "G" and (resid 12 through 35 or resid 49 through 118))
d_2ens_5(chain "I" and (resid 12 through 35 or resid 49 through 118))

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_1SERSERGLYGLYAJ2 - 2141 - 213
d_12ens_1ACTACTACTACTAL301
d_21ens_1SERSERGLYGLYLA2 - 2141 - 213
d_22ens_1ACTACTACTACTLK301
d_11ens_2GLNGLNPROPROBC1 - 2211 - 221
d_21ens_2GLNGLNSERSERHB1 - 1361 - 136
d_22ens_2THRTHRTHRTHRHB143 - 199143 - 199
d_23ens_2TYRTYRPROPROHB202 - 221202 - 221
d_11ens_3SERSERVALVALCF2 - 2071 - 206
d_21ens_3SERSERVALVALEH2 - 2071 - 206
d_11ens_4GLNGLNGLUGLUDG1 - 2201 - 220
d_21ens_4GLNGLNSERSERFI1 - 1351 - 135
d_22ens_4GLYGLYGLYGLYFI142142
d_23ens_4ALAALAALAALAFI144 - 166144 - 166
d_24ens_4SERSERSERSERFI169 - 194169 - 194
d_25ens_4GLNGLNGLUGLUFI200 - 220200 - 220
d_11ens_5METMETMETMETGD12 - 351 - 24
d_12ens_5THRTHRASPASPGD49 - 11838 - 107
d_21ens_5METMETMETMETIE12 - 351 - 24
d_22ens_5THRTHRASPASPIE49 - 11838 - 107

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixベクター
1given(0.0136726447888, -0.971898927017, 0.235001137118), (0.999775739852, 0.0170890469305, 0.0125073769944), (-0.0161718517416, 0.234777426806, 0.971914621288)-23.1745799774, 32.4363148475, 50.5160710399
2given(0.0156694092829, -0.977534231743, 0.210193471315), (0.999831272995, 0.0133031100107, -0.012666996694), (0.0095861960093, 0.210356490355, 0.977577747195)-23.9330237482, 31.5901637082, 52.018228888
3given(0.0416189255875, 0.999110037507, 0.0068555076964), (-0.979726829813, 0.0394637905524, 0.196412698622), (0.195967354367, -0.0148910103105, 0.980497350243)-29.4604895115, -34.2095114392, -44.1455767851
4given(0.0431872285166, 0.998553921824, 0.0320145045704), (-0.977084252732, 0.0355301665612, 0.209866553618), (0.208425589495, -0.0403444230838, 0.97720576194)-31.479272488, -36.149967031, -44.8436983222
5given(0.0239279361694, 0.998552579627, 0.0481684501537), (-0.990963055982, 0.0173298557446, 0.133010893457), (0.131983618487, -0.0509158307347, 0.989943383549)-32.7478604269, -32.4572952184, -50.6067350743

-
要素

-
タンパク質 , 1種, 2分子 GI

#3: タンパク質 Conglutin


分子量: 14509.228 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Arachis hypogaea (トウジンマメ)
細胞株 (発現宿主): ovary
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: Q647G9

-
抗体 , 4種, 8分子 LAHBCEDF

#1: 抗体 16A8 light chain


分子量: 23318.846 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): ovary
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#2: 抗体 16A8 heavy chain


分子量: 23899.611 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): ovary
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#4: 抗体 13D9 light chain


分子量: 22708.002 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): expi293 / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 13D9 heavy chain


分子量: 23792.859 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): expi293 / 発現宿主: Homo sapiens (ヒト)

-
非ポリマー , 2種, 151分子

#6: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H3O2
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 149 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

-
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: 3.02 Å3/Da / 溶媒含有率: 59.3 %
結晶化温度: 292 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 00 mM Bis Tris pH 5.25, 75 mM Ammonium Acetate, 16% PEG 10,000

-
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: APS / ビームライン: 21-ID-D / 波長: 1.12713 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2022年9月18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: 1.12713 Å / 相対比: 1
反射解像度: 2.68→44.96 Å / Num. obs: 76577 / % possible obs: 99.4 % / 冗長度: 4.6 % / Biso Wilson estimate: 75.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Net I/σ(I): 22
反射 シェル解像度: 2.68→2.78 Å / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 7559 / CC1/2: 0.798

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
autoPROC1.05data processing
XDSVERSION Jan 10, 2022 BUILT=20220220データ削減
Aimless0.7.9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 / 解像度: 2.68→44.96 Å / SU ML: 0.4171 / 交差検証法: FREE R-VALUE / 位相誤差: 27.1369
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.239 3911 5.11 %
Rwork0.1941 71984 -
obs0.1964 76577 99.29 %
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: 96.8 Å2
精密化ステップサイクル: LAST / 解像度: 2.68→44.96 Å
タンパク質核酸リガンド溶媒全体
原子数14367 0 8 149 14524
拘束条件タイプ: f_bond_d / Dev ideal: 0.0106 / 数: 14679
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2JAX-RAY DIFFRACTIONTorsion NCS1.15572866255
ens_2d_2CBX-RAY DIFFRACTIONTorsion NCS1.12786039035
ens_3d_2FCX-RAY DIFFRACTIONTorsion NCS1.23519447499
ens_4d_2GDX-RAY DIFFRACTIONTorsion NCS1.75238635726
ens_5d_2DGX-RAY DIFFRACTIONTorsion NCS1.11467220309
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.710.3681390.3282526X-RAY DIFFRACTION100
2.71-2.750.3471420.3062605X-RAY DIFFRACTION100
2.75-2.780.3421340.2872560X-RAY DIFFRACTION100
2.78-2.820.2671340.2582612X-RAY DIFFRACTION100
2.82-2.860.2941490.2622528X-RAY DIFFRACTION100
2.86-2.90.2941490.2622528X-RAY DIFFRACTION100
2.9-2.950.3171210.242583X-RAY DIFFRACTION100
2.95-30.2811230.2472621X-RAY DIFFRACTION100
3-3.050.3321220.26132581X-RAY DIFFRACTION100
3.05-3.10.291290.2692600X-RAY DIFFRACTION100
3.1-3.160.331170.2822597X-RAY DIFFRACTION100
3.16-3.230.3361750.282520X-RAY DIFFRACTION100
3.23-3.30.311630.2532540X-RAY DIFFRACTION99
3.3-3.380.2741340.242585X-RAY DIFFRACTION99
3.38-3.460.2781480.2262566X-RAY DIFFRACTION99
3.46-3.550.2631240.2252581X-RAY DIFFRACTION99
3.55-3.660.2731350.2252542X-RAY DIFFRACTION98
3.66-3.780.2991390.2272593X-RAY DIFFRACTION99
3.78-3.910.2681360.2252599X-RAY DIFFRACTION100
3.91-4.070.2331540.1882595X-RAY DIFFRACTION100
4.07-4.260.2091530.1642603X-RAY DIFFRACTION100
4.25-4.480.2131330.1492645X-RAY DIFFRACTION100
4.48-4.760.1791380.1422599X-RAY DIFFRACTION100
4.76-5.120.2031580.1432635X-RAY DIFFRACTION100
5.12-5.640.1841360.1572652X-RAY DIFFRACTION100
5.65-6.450.2141400.1792612X-RAY DIFFRACTION98
6.45-8.120.2241390.1832626X-RAY DIFFRACTION97
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)
16.341138641480.805204660639-0.6884851006733.34330870479-0.7324246657433.353124857860.1833057901240.153621923163-0.0268743994078-1.12081990988-0.339375027776-1.204180343770.6495728240120.6372804342840.2571722843880.8072102015660.1789376162120.322013826940.4701209163550.06971351584650.972544230596-26.1303715017-31.253377357525.6918112258
26.23275284385-0.166945398473-3.522956123854.90759622857-2.009145438886.15599511257-0.255477564860.436151229276-0.620090944044-1.40084566026-0.0141273276419-0.6395650941290.973167903261-0.01337613681270.17734988760.9001207133890.1322950449380.3892271117370.5483471275150.00154816162530.920426490666-29.1461472531-35.063429954224.8751176744
31.568550066221.96684494016-0.23160055986.32166368699-2.975816664722.37335874295-0.4867336974250.302925027144-0.208891761238-0.1070253574540.2848144681580.3152133985390.358368409905-0.2780922329730.1411910229120.7597218158480.02892581910780.309614679960.6162496862690.1752320071680.76939676327-27.6078692341-2.7214812898211.2670180768
47.414352242662.6571356404-3.59998082795.75616015708-1.466623836837.19329297921-0.05597749119950.01757431417080.461026288488-0.7023220059740.178048629234-0.9525124127980.03113550057150.436881239943-0.1339710419490.5394220901370.04030591308250.2266563388920.6124097625170.117007398710.713500362897-22.3404232132.2756009446912.2275283248
55.256598480483.942555694633.82976146655.180832605190.3812897359655.11306605382-0.098694276957-0.4643373796360.694775256677-0.111962870272-0.2352496837620.642060987732-0.463999698727-0.8172524193230.2330647450440.4773517488390.1169970257260.1495024622460.4182116930030.03210774700840.512410974661-47.0689819064-15.743479469631.9673348242
64.314397588540.5516299189050.4540175868965.84419834502-0.7770355596122.87242499788-0.1523834886420.305062250416-0.336717142457-0.8117743266310.176149912510.6439299541850.5138990196690.02732046234760.02558867366960.5373445334040.02173127790410.08614614974310.37510632542-0.02168941368240.444251892509-51.7194935726-29.460547793330.4330217973
73.620808889351.18777102108-0.05505044126219.131992552-0.551789582373.415836062270.04414214443370.227793235430.0338591143948-0.212779254789-0.128096139455-1.548363084970.1317373661650.5437934614770.143114579030.4356135054940.04539346835950.1811930063250.4366899041890.03030907116350.615700232145-36.7400420646-21.637949124832.498452483
85.58238084282.661059756880.04989488520045.951338493740.3932938117642.339719632370.223862759868-0.735807217323-0.2481330056990.747771281189-0.2228423517980.03919962229030.3017684168-0.0694765213229-0.01983520524590.5415695485320.04313591032120.1001945372410.4712170673540.05585826582340.387014868525-46.5129420207-26.546129010539.9600647649
91.758931755063.547731710180.4060237969427.814837533251.386919637673.2205420553-0.0232271608498-0.0380394831813-0.310219501232-0.1174985266410.0594266731548-0.4820518009690.0389285823109-0.032783961865-0.05617966845560.4007799681370.1139428193360.1292871365680.422380188474-0.009840596855180.517997347144-40.1250073115-19.862213605634.8334097978
102.269310276891.56771579917-1.075518709764.40546282671-2.497290518542.88767265113-0.2761702570620.02282524457350.00980011019841-0.4339234428380.280176914024-0.2117755990180.297972695224-0.0510184903916-0.02810271724620.3972532425330.0933520036560.06301994014680.448448265703-0.03391914520740.339616171869-41.1345413082-20.636360108430.0950927224
116.60676015734-2.8559228593-0.8289826548313.542232425226.253176789882.073849081821.312400579740.998878236830.843976143601-1.865251525710.638672140064-0.335928904517-1.518653948170.652848700525-2.016570603461.14717451530.03818993474890.1991709847560.8670138012130.1306079278580.804509947785-33.65012065373.855526354112.8008695717
124.711085390532.091559536670.468284908434.073677328480.1684695931954.44286623597-0.3007971382810.449522866827-0.00763934979924-0.5549622734890.4394173565110.1901253159660.0574559083864-0.102897350083-0.1130703433350.5591356950420.02789648773950.1489252540050.4727515803890.1127370557280.613947317781-36.9577916912-3.5355897241516.4281352634
135.877735795672.42664226234-5.168609126855.06456913198-0.1798051402135.78370308146-0.3360588623421.3595101840.578131142586-1.433538118570.5742199648881.1227396171-0.712104361216-0.724752116795-0.2344822957440.932900525977-0.0737464767449-0.1304923886720.9390208589320.3440504996650.834307621411-44.4324939978-1.047943558229.41152888649
144.2503034538-0.4945820105211.477531574354.72846738338-0.3603586964923.97536504286-0.1370753298940.039994717318-0.00615647728945-0.07535292738080.0597161849181-0.581627391263-0.04840131136740.2045897949050.09240870859670.383442864063-0.09322788917410.03668184581250.419233095306-0.01389970836380.447126826795-55.774627601116.6083629216-19.9428047588
154.53287110405-0.777229235547-1.911550997492.682605409070.3854085175213.711049214760.1359899931860.166464602317-0.0419530680874-0.241422059848-0.0407421104392-0.6179516939780.3846522038170.5021522386890.01400287656310.527543462512-0.006931036070180.04164618490640.451332244983-0.01368227766260.547000427097-46.82870318539.28262712209-29.6790807536
167.228056670622.653257021890.6160849115287.15467247002-0.5977205673347.80029801828-0.1296537392910.6740988427891.23058075039-1.130651584080.0820922173265-0.542743272952-0.1673854705340.5696044876180.0448576639870.6466550866680.1560791768590.1634145854840.7177369024260.1580931665980.955906672027-34.45664697986.79394083478-40.268553257
174.955871342582.454134379641.668869093073.87040372259-0.3295173472387.0498001869-0.2299869925830.0349843981104-0.0440130359981-0.177719120236-0.1804996546360.9082357169730.149197433495-0.1748359997740.1877768587480.5449194580530.02669627456050.2044968851490.4413796435790.1004818359990.611371216314-48.4468908053-56.124532110445.7997272499
181.99454864371-4.42336899998-0.1857633446976.2259717488-4.372611154664.1501210629-0.6662559802581.36211852942-1.36450861027-2.547518854740.308717553209-1.645722697442.237157960980.7151768002490.1316479107031.681218000420.1170765334120.1795141037310.86641213856-0.2213729970322.02375118-45.7414736425-70.577473570435.3328901413
194.6941141516-0.2964419744731.594627314762.076874116513.355652532062.25906183350.09575972089330.371016230637-0.320727200132-0.544712384711-0.5160424537770.3856842517130.571703284993-0.5992903632040.5527148885560.914900755218-0.01757556377890.2028263055990.5663943619710.1020102945280.729769236894-55.1721265355-54.878641073341.4815277003
206.63346816238-2.31891938717-0.9476655569617.140661905940.1252846944138.83572397264-0.134081607730.0531423852421-0.294920399278-1.32066801074-0.121713616294-0.7750485206910.9770421333110.9427291645660.007625732985120.979625617071-0.003770115160280.3618691772870.517545256090.1228190347790.773836093809-39.8918214214-56.665944705639.4355598779
212.1188109258.788041903144.372885707136.176673358731.863947423142.225441813910.5155217066860.804190594362-1.75818142463-0.398612083008-0.0689882062218-0.9196022371220.4913781534920.393643943569-0.3419028486840.7740276718650.06605940567660.2290908798680.591048297886-0.0418536479890.849822939486-44.4010965187-45.682510207436.2479636111
225.05627234113-0.5558778826875.682527538458.20798391453.528111107119.66378543573-0.1201344704071.496001343440.379021391198-0.04549764618440.0995751917975-0.102413980409-0.3630010585780.760461997641-0.009634178494150.475418399526-0.1258509369850.1313377320920.7178624740430.1239938641690.501837141419-87.343924107421.0934923253-8.50226736482
238.341400359492.42077641756-2.82326977741.993139332459.040318045332.00518444672-0.5946610787150.5357137386151.41550474002-0.878165201957-1.383367288823.76408037155-0.267233713501-3.483850935081.844803670711.115926994260.111023514164-0.1650949009791.58811836375-0.4107764557231.62520114759-102.12381865117.9061603301-17.8035295821
242.07048478803-1.08482269875-4.997794758412.338371796931.814044663097.53957363294-0.1088943178910.3097590666921.43776664153-0.605912752790.265009976453-0.226971158179-1.097382302150.494975808231-0.327915808730.602545885086-0.1806571623120.01583612381430.6650247512560.1590029230770.86079365222-86.792770623426.7138491323-14.0680523001
255.00091426833-1.82187434575-4.693189856767.09798335247-0.3652712235756.3657652474-0.6013350329291.30511958983-0.854087468022-0.2325228188650.3942758004440.412148501141.02209444842-0.670758296350.2484082058290.471488098438-0.1255824422120.007550821052630.829924515843-0.09311394951050.701658033734-88.386282706911.0654894999-13.7708464165
262.1621709844-1.94616956871-0.1387737286489.75146293789-1.512938240415.58839280063-0.5046610708410.968043594313-0.5661303615220.4029326558221.004508039091.06877926871-0.11807649731-1.10206382809-0.2884080495640.376646288891-0.118261526860.01619822739160.7828249091750.07918530853510.626641860297-78.435273561916.3127589048-18.3365426743
271.765562685491.211926151881.227576729424.40194569912-1.735357390583.510131678960.103953619405-0.154646913709-0.1878330165440.0768494347703-0.1057658204080.009052096831730.196930181-0.132381936289-0.003925754662260.466531350985-0.0145421668460.1756911580340.403109935380.008941693653790.500147769193-48.1938488447-71.695198199762.5227256819
289.24387559185-7.243682613123.159724955138.90832187172-7.233813001838.316211988650.1765201409470.6607859371280.32615561206-1.55864101846-1.02356969803-1.785994796641.294195531670.4368882102040.7388126389260.7600123006730.1647452514170.378198533940.5873134081890.1526455756321.07483569635-38.1827260921-70.914666956455.125125375
291.816895547470.827931163072-0.1345364364885.9658287155-3.519912892076.08909466450.0276097833775-0.0768999999607-0.292091720709-0.285314451125-0.229413531014-0.3367637879190.4530517717670.1665935402630.233392435220.474312399332-0.03773418469740.1714551177730.366090206630.003278904751420.57997818091-46.9920897322-71.814005753962.4910690508
303.604332197271.192823539230.7132793213274.056775319470.1310876140024.784473788570.129724715112-1.16851371285-0.08529576905341.30979984040.235491131218-0.7851564078170.6776395085180.777116552716-0.3704567500530.8999530041070.036032426275-0.2824250810620.8138820770230.0363861528730.68531709935-44.2043727736-79.526592863696.4454451177
313.923347473750.121691111767-1.448944455313.912820625232.413971913456.295688254230.0133007130765-1.49324362573-0.07756530871052.437890626420.443862572249-0.1669367149721.786959634140.333587754-0.5386472311891.4762795538-0.00900575527566-0.24898471190.9925271016110.08836809719710.755157972041-47.4794329216-81.1210755186103.32989827
320.7591620901290.287983570643-2.330039821190.7214416718370.1128236631758.467096684620.0815881240223-0.7241781234920.382082639318-0.048269705566-0.104204878103-0.835361569183-1.194241449961.30104474335-0.08827693819330.766629536273-0.2997849120280.1100720531290.700159516595-0.07809117798370.977590399408-39.8287516256-51.259975447178.4590966583
334.71307424021-0.6986532053020.1994228538994.34356845656-0.3745839838286.586020381240.4774832755430.1070706532721.125855601040.182255952957-0.314109848639-0.588715251619-0.9424251512560.291733895282-0.08741439800850.556882919124-0.06151227870990.1273779685820.3702417996980.02904871029550.776301629536-44.112259043-49.814539021167.6127230556
341.28273738165-0.5970820201550.1351137438141.73285380209-1.137876997665.510133962770.209559168135-0.250661098250.5228387221340.221326278381-0.255809434751-0.29868730749-0.6730076832690.197305727806-0.03042369248860.513733618936-0.1299915115480.1186082042130.419450943024-0.05205691812210.746963482152-43.9950338888-54.057447041174.2796953959
350.472496683099-0.514725202148-0.3751926444981.96775895086-1.459940653271.48392478295-0.137084406568-0.4120701509470.05878342420150.7339781800050.292625348262-0.2424992348990.4360640102570.433148937181-0.1409596583950.971863878628-0.111130650444-0.3293300348581.07506169152-0.2074352831070.934288817612-35.5728948114-71.2886450558101.753973344
361.97579717247-6.767390752270.4104231865014.4288438413-0.7702232088780.623305636043-0.0568744160842-0.08016801882850.9755324941220.06589333645880.314740871904-0.9634486821930.9038248831920.0113959089512-0.01670615623550.949798735293-0.194957229396-0.1855705815810.93221169626-0.1939312287971.09345863665-32.4098446674-68.039738410191.3220201023
372.636336922961.3862027062-0.1091569152431.87401065570.2743608751948.593706765110.297789274692-0.273662376375-0.2530710889850.197320683780.667570943629-0.4997642339591.19427059310.300080125944-1.129016903120.876293050446-0.202740339406-0.2047375980510.666081327921-0.1574937441960.952879998287-41.6814343893-69.425794928995.3467336712
388.97875081221-7.985023755916.477586586157.24550910107-6.986797855056.34757991531-0.879202519398-0.2946622598490.7931671775150.6412226222440.682589839668-2.16043379931-0.4757399364230.8816531359980.1569390416550.825894765112-0.013967081407-0.1189162774630.95441938968-0.3716074202191.10028342264-28.3521428021-66.251882836598.3532609372
398.31139993024-1.38555181908-1.402099510683.922856494960.7249280306496.55307157456-0.2523749886550.0867190339817-0.0169802641180.117145237336-0.05976156259250.5034976337120.252347945115-0.2827765298830.2543181404320.321104667969-0.002088416504070.03330789750890.2925961000740.005325985720840.443633606626-103.11985274219.68482215567.45313044245
402.465361617012.7367196448-8.343822085864.872719160560.01444064679298.20870637029-0.1083467624261.316745743392.085220618620.2050314589510.8436171510650.70745979042-0.144226870611-0.849679471089-0.8394928015610.3371080012650.104033283234-0.07089514147330.6551109977820.2507417812260.661767918194-98.441786717625.467255289610.9286140782
413.26992062421.143619288090.2904170970333.365518203360.1554474780588.453014972490.0445145132188-0.69601507105-0.6296989296391.038377480120.109047161327-0.7364360812280.5355123030140.253185757854-0.1981602505220.7157821430070.150510753278-0.09170852429950.5547564320570.1498214400310.572152244807-110.37274457623.963448248444.8559446932
423.981240552671.896022868351.355264141464.994007677940.5259109085659.063596090750.0572866683964-0.320508102957-0.6658620701940.510711222639-0.053294719415-0.429103235909-0.05060839636980.379209501015-0.152202743710.5062562736020.151143098074-0.1070760603990.5546663477720.1381147316210.670795448032-109.25393563527.088588423739.734533855
431.707147824170.778998603288-0.5785944250791.9512902042-0.1331510659156.765575639310.0605827517793-0.654410930913-0.2228893271850.856029888707-0.263901706339-0.39096955423-0.4222672352330.1227241464750.2191464695250.9135611280330.127564315317-0.09639536954870.6853477532290.1751824718160.648592778025-111.74174655628.688692137151.5556938284
445.56882205952-0.5686903150460.6496137669632.786999909240.7778155752647.37827350795-0.360361244232-0.781246887121-0.322125407140.2698492909810.123318028868-0.5780015732730.2953390518680.7472678891040.2045135484430.3649539658260.09844839680220.05378435686770.5753916120650.133967523680.624506408113-82.264329754319.275537454516.057139932
452.828207750982.26477297391-1.475123639313.462471976450.5606699757084.066100807270.0883930288401-0.639564527659-1.883024039290.920813927198-0.316912522977-1.271422379770.8584257630271.117114056260.2732198629621.024412892090.290748191143-0.3199158036271.000233311240.199764304091.31400952235-99.02482703514.93898443247.2045574818
464.17207003657-1.02327735628-1.104308769735.967790112421.081761694933.61479022935-0.02712163336610.192961941481-0.339727949769-0.1175142685620.1366356879180.1775250643181.00473781437-0.264127215274-0.08049428859840.622682023976-0.153543325237-0.05049527930960.417446754125-0.02570135863940.451472926204-63.2857598978-4.07978568704-25.8068394722
473.80085047167-0.433502076637-1.687510104752.6608679278-0.04958192139782.84815060113-0.0851970187680.560392541364-0.228338220677-0.610817023375-0.00223061811731-0.1091926705170.595259913397-0.07122352432140.1427358867840.800338082314-0.05850348789090.03350517748230.419780244588-0.03775854977670.551874773206-56.1305228677-2.83711562597-31.4076841813
483.904485695963.89553530257-0.2513244553374.661639753292.196900007065.382000057320.299815508853-0.603278627941-1.10416765349-0.369893511951-0.488202324451-1.775658805761.002902958620.4298205956580.1478520988990.9831504188140.2005595409060.1842797390560.6300788392040.2346467090661.12666271862-34.6165038914-9.84375469292-36.1203734224
493.04130951593-0.5913244647270.4513636805450.2395512827580.1667882101021.192813564330.2125210021890.302735914027-2.832362989910.05320765152830.230986900127-3.028058049340.5030509686450.691360062566-0.3254142988770.8540612169750.1173340949830.2546475901531.0125696308-0.08768946949542.30420581263-23.4857830265-10.7405814324-38.6249617707
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 'L' and (resid 2 through 48 )LA2 - 481 - 47
22chain 'L' and (resid 49 through 103 )LA49 - 10348 - 99
33chain 'L' and (resid 104 through 130 )LA104 - 130100 - 126
44chain 'L' and (resid 131 through 214 )LA131 - 214127 - 210
55chain 'H' and (resid 1 through 17 )HC1 - 171 - 17
66chain 'H' and (resid 18 through 33 )HC18 - 3318 - 33
77chain 'H' and (resid 34 through 45 )HC34 - 4534 - 45
88chain 'H' and (resid 46 through 83 )HC46 - 8346 - 83
99chain 'H' and (resid 84 through 100 )HC84 - 10084 - 100
1010chain 'H' and (resid 101 through 128 )HC101 - 128101 - 128
1111chain 'H' and (resid 129 through 143 )HC129 - 143129 - 141
1212chain 'H' and (resid 144 through 192 )HC144 - 192142 - 190
1313chain 'H' and (resid 193 through 221 )HC193 - 221191 - 219
1414chain 'B' and (resid 1 through 100 )BD1 - 1001 - 100
1515chain 'B' and (resid 101 through 143 )BD101 - 143101 - 137
1616chain 'B' and (resid 144 through 222 )BD144 - 222138 - 214
1717chain 'G' and (resid 12 through 34 )GE12 - 341 - 23
1818chain 'G' and (resid 35 through 50 )GE35 - 5024 - 28
1919chain 'G' and (resid 51 through 71 )GE51 - 7129 - 49
2020chain 'G' and (resid 72 through 107 )GE72 - 10750 - 85
2121chain 'G' and (resid 108 through 118 )GE108 - 11886 - 96
2222chain 'I' and (resid 12 through 33 )IF12 - 331 - 22
2323chain 'I' and (resid 34 through 50 )IF34 - 5023 - 27
2424chain 'I' and (resid 51 through 71 )IF51 - 7128 - 48
2525chain 'I' and (resid 72 through 106 )IF72 - 10649 - 83
2626chain 'I' and (resid 107 through 118 )IF107 - 11884 - 95
2727chain 'C' and (resid 2 through 48 )CG2 - 481 - 47
2828chain 'C' and (resid 49 through 61 )CG49 - 6148 - 60
2929chain 'C' and (resid 62 through 106 )CG62 - 10661 - 105
3030chain 'C' and (resid 107 through 172 )CG107 - 172106 - 171
3131chain 'C' and (resid 173 through 207 )CG173 - 207172 - 206
3232chain 'D' and (resid 1 through 17 )DH1 - 171 - 17
3333chain 'D' and (resid 18 through 76 )DH18 - 7618 - 76
3434chain 'D' and (resid 77 through 127 )DH77 - 12777 - 127
3535chain 'D' and (resid 128 through 153 )DH128 - 153128 - 146
3636chain 'D' and (resid 154 through 173 )DH154 - 173147 - 164
3737chain 'D' and (resid 174 through 192 )DH174 - 192165 - 183
3838chain 'D' and (resid 193 through 220 )DH193 - 220184 - 206
3939chain 'E' and (resid 2 through 92 )EI2 - 921 - 91
4040chain 'E' and (resid 93 through 106 )EI93 - 10692 - 105
4141chain 'E' and (resid 107 through 151 )EI107 - 151106 - 150
4242chain 'E' and (resid 152 through 172 )EI152 - 172151 - 171
4343chain 'E' and (resid 173 through 213 )EI173 - 213172 - 212
4444chain 'F' and (resid 1 through 119 )FJ1 - 1191 - 119
4545chain 'F' and (resid 120 through 222 )FJ120 - 222120 - 217
4646chain 'A' and (resid 2 through 48 )AK2 - 481 - 47
4747chain 'A' and (resid 49 through 130 )AK49 - 13048 - 126
4848chain 'A' and (resid 131 through 176 )AK131 - 176127 - 172
4949chain 'A' and (resid 177 through 214 )AK177 - 214173 - 210

+
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://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