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- PDB-7mph: GRB2 SH2 Domain with Compound 7 -

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基本情報

登録情報
データベース: PDB / ID: 7mph
タイトルGRB2 SH2 Domain with Compound 7
要素Growth factor receptor-bound protein 2
キーワードPROTEIN BINDING / Inhibitor / Complex / growth factor receptor / Ras-MAPK signaling cascade
機能・相同性
機能・相同性情報


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / neurotrophin TRKA receptor binding / COP9 signalosome / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / neurotrophin TRKA receptor binding / COP9 signalosome / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / negative regulation of natural killer cell mediated cytotoxicity / MET activates PTPN11 / MET activates RAP1 and RAC1 / vesicle membrane / Signaling by LTK / MET activates PI3K/AKT signaling / CD28 dependent Vav1 pathway / Signal regulatory protein family interactions / epidermal growth factor receptor binding / Regulation of KIT signaling / PI-3K cascade:FGFR3 / natural killer cell mediated cytotoxicity / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / positive regulation of actin filament polymerization / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / regulation of MAPK cascade / RET signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K events in ERBB2 signaling / PI3K Cascade / signal transduction in response to DNA damage / SOS-mediated signalling / Role of LAT2/NTAL/LAB on calcium mobilization / Activated NTRK3 signals through RAS / fibroblast growth factor receptor signaling pathway / Activated NTRK2 signals through RAS / Interleukin receptor SHC signaling / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signal attenuation / Signalling to RAS / GAB1 signalosome / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / ephrin receptor binding / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / phosphotyrosine residue binding / myelination / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / FCERI mediated Ca+2 mobilization / GRB2 events in ERBB2 signaling / Downstream signal transduction / insulin-like growth factor receptor signaling pathway / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / T cell activation / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to ionizing radiation / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling
類似検索 - 分子機能
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
類似検索 - ドメイン・相同性
Chem-ZLY / Growth factor receptor-bound protein 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2 Å
データ登録者Sun, L. / Schonbrunn, E.
引用ジャーナル: Bioorg.Med.Chem.Lett. / 年: 2021
タイトル: Synthesis and structural characterization of a monocarboxylic inhibitor for GRB2 SH2 domain.
著者: Xiao, T. / Sun, L. / Zhang, M. / Li, Z. / Haura, E.B. / Schonbrunn, E. / Ji, H.
履歴
登録2021年5月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年9月22日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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

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集合体

登録構造単位
A: Growth factor receptor-bound protein 2
B: Growth factor receptor-bound protein 2
C: Growth factor receptor-bound protein 2
D: Growth factor receptor-bound protein 2
E: Growth factor receptor-bound protein 2
F: Growth factor receptor-bound protein 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,83136
ポリマ－66,0516
非ポリマー5,78030
水2,000111
1
A: Growth factor receptor-bound protein 2
ヘテロ分子

F: Growth factor receptor-bound protein 2
ヘテロ分子

E: Growth factor receptor-bound protein 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,70616
ポリマ－33,0253
非ポリマー2,68113
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area6600 Å2
ΔGint-69 kcal/mol
Surface area13970 Å2
手法PISA
2
C: Growth factor receptor-bound protein 2
D: Growth factor receptor-bound protein 2
ヘテロ分子

B: Growth factor receptor-bound protein 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,12520
ポリマ－33,0253
非ポリマー3,09917
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area7020 Å2
ΔGint-111 kcal/mol
Surface area14110 Å2
手法PISA
単位格子
Length a, b, c (Å)61.885, 87.102, 136.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 59 through 70 or (resid 71...
21(chain B and (resid 59 through 68 or (resid 69...
31(chain C and (resid 59 through 66 or (resid 67...
41(chain D and (resid 59 through 66 or (resid 67...
51(chain E and (resid 59 through 71 or (resid 72...
61(chain F and (resid 59 through 66 or (resid 67...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALA(chain A and (resid 59 through 70 or (resid 71...AA59 - 702 - 13
12GLUGLUGLUGLU(chain A and (resid 59 through 70 or (resid 71...AA71 - 7214 - 15
13GLYGLYPHEPHE(chain A and (resid 59 through 70 or (resid 71...AA58 - 1471 - 90
14GLYGLYPHEPHE(chain A and (resid 59 through 70 or (resid 71...AA58 - 1471 - 90
15GLYGLYPHEPHE(chain A and (resid 59 through 70 or (resid 71...AA58 - 1471 - 90
16GLYGLYPHEPHE(chain A and (resid 59 through 70 or (resid 71...AA58 - 1471 - 90
21PROPROALAALA(chain B and (resid 59 through 68 or (resid 69...BB59 - 682 - 11
22LYSLYSGLUGLU(chain B and (resid 59 through 68 or (resid 69...BB69 - 7212 - 15
23GLYGLYILEILE(chain B and (resid 59 through 68 or (resid 69...BB58 - 1511 - 94
24GLYGLYILEILE(chain B and (resid 59 through 68 or (resid 69...BB58 - 1511 - 94
25GLYGLYILEILE(chain B and (resid 59 through 68 or (resid 69...BB58 - 1511 - 94
26GLYGLYILEILE(chain B and (resid 59 through 68 or (resid 69...BB58 - 1511 - 94
31PROPROPROPRO(chain C and (resid 59 through 66 or (resid 67...CC59 - 662 - 9
32ARGARGGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC67 - 7210 - 15
33GLYGLYGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC58 - 1521 - 95
34GLYGLYGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC58 - 1521 - 95
35GLYGLYGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC58 - 1521 - 95
36GLYGLYGLUGLU(chain C and (resid 59 through 66 or (resid 67...CC58 - 1521 - 95
41PROPROPROPRO(chain D and (resid 59 through 66 or (resid 67...DD59 - 662 - 9
42ARGARGGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD67 - 7210 - 15
43GLYGLYGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD58 - 1521 - 95
44GLYGLYGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD58 - 1521 - 95
45GLYGLYGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD58 - 1521 - 95
46GLYGLYGLUGLU(chain D and (resid 59 through 66 or (resid 67...DD58 - 1521 - 95
51PROPROGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE59 - 712 - 14
52GLUGLUGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE7215
53GLYGLYGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE58 - 1521 - 95
54GLYGLYGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE58 - 1521 - 95
55GLYGLYGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE58 - 1521 - 95
56GLYGLYGLUGLU(chain E and (resid 59 through 71 or (resid 72...EE58 - 1521 - 95
61PROPROPROPRO(chain F and (resid 59 through 66 or (resid 67...FF59 - 662 - 9
62ARGARGGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF67 - 7210 - 15
63PROPROGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF59 - 1522 - 95
64PROPROGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF59 - 1522 - 95
65PROPROGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF59 - 1522 - 95
66PROPROGLUGLU(chain F and (resid 59 through 66 or (resid 67...FF59 - 1522 - 95

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要素

#1: タンパク質
Growth factor receptor-bound protein 2 / Adapter protein GRB2 / Protein Ash / SH2/SH3 adapter GRB2


分子量: 11008.441 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GRB2, ASH / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62993
#2: 化合物
ChemComp-ZLY / (4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid


分子量: 652.779 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C38H44N4O6 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 13 / 由来タイプ: 合成 / 式: C2H6O2
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 11 / 由来タイプ: 合成 / 式: SO4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 111 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.78 Å3/Da / 溶媒含有率: 55.81 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5
詳細: 12.4mg/mL GRB2 SH2 domain, 0.1mM Bis-Tris pH 5.5, 2M Ammonium Sulphate

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データ収集

回折平均測定温度: 291 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: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2020年8月9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: 1.0332 Å / 相対比: 1
反射解像度: 2→47.32 Å / Num. obs: 50672 / % possible obs: 100 % / 冗長度: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Net I/σ(I): 9.8 / Num. measured all: 336368 / Scaling rejects: 101
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.056.73.2892498437020.4451.3663.5650.6100
8.94-47.325.90.03238886590.9990.0140.03540.799.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2-3874_3874精密化
Aimless0.5.1データスケーリング
PDB_EXTRACT3.27データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1CJ1

1cj1


解像度: 2→45.83 Å / SU ML: 0.37 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 36.24 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2773 1996 3.95 %
Rwork0.2313 48501 -
obs0.2331 50497 99.79 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 153.38 Å2 / Biso mean: 66.3428 Å2 / Biso min: 37.39 Å2
精密化ステップサイクル: final / 解像度: 2→45.83 Å
タンパク質核酸リガンド溶媒全体
原子数4471 0 394 111 4976
Biso mean--60.52 55.15 -
残基数----563
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2359X-RAY DIFFRACTION15.48TORSIONAL
12B2359X-RAY DIFFRACTION15.48TORSIONAL
13C2359X-RAY DIFFRACTION15.48TORSIONAL
14D2359X-RAY DIFFRACTION15.48TORSIONAL
15E2359X-RAY DIFFRACTION15.48TORSIONAL
16F2359X-RAY DIFFRACTION15.48TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.4731400.44453405354599
2.05-2.110.42221390.407633933532100
2.11-2.170.39161400.369734263566100
2.17-2.240.42451420.333434103552100
2.24-2.320.32281400.303234113551100
2.32-2.410.3731410.29334283569100
2.41-2.520.31531430.287934403583100
2.52-2.650.3461410.275534323573100
2.65-2.820.31021430.279134743617100
2.82-3.040.32281420.264934503592100
3.04-3.340.28311420.241634893631100
3.34-3.830.26481450.208735073652100
3.83-4.820.21951460.170935413687100
4.82-45.830.23511520.199336953847100
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)
17.82291.4789-2.64988.3047-1.88235.640.18980.49060.46861.04630.24081.0533-1.4345-1.7262-0.40590.90830.30640.17671.0031-0.02720.54587.72713.555731.8412
27.7037-0.35730.38180.0157-0.02340.0167-0.3153-2.07571.8770.6993-0.10991.2377-0.5895-1.24160.33812.050.6490.56531.0159-0.30851.05694.439125.730730.3674
34.6853-0.596-0.67695.6150.04716.6470.1319-0.02130.21660.39250.14970.174-0.7429-0.0208-0.27940.72920.04310.05160.3676-0.02820.374215.526415.076721.8936
44.5041-1.27115.18033.1271-2.9427.1761-0.4804-0.88451.55310.2363-0.3031-0.1772-3.0122-1.03440.72891.21470.0824-0.06480.6072-0.05050.631411.583525.946918.4371
57.8376-3.3557.068.3443-5.62137.5571-0.348-0.8106-0.2034-0.19260.74120.4792-1.26410.1708-0.37070.7311-0.1021-0.03620.66640.00520.381433.51743.193518.6046
68.1882-5.42440.53696.73230.25296.8501-0.2048-0.3638-1.03750.3776-0.17881.04041.2635-1.4160.41680.9187-0.36520.05050.952-0.05690.789524.775135.546716.3843
76.2628-4.2326-5.21225.68354.26678.52280.10960.3709-0.9904-0.4570.17770.242-0.16130.2195-0.29390.5961-0.0796-0.08630.59350.02030.472738.013642.647312.2481
88.83860.5409-2.36247.3884-2.77464.4692-0.4787-1.3737-0.70860.10180.22120.66270.8833-0.87620.18210.476-0.22050.04170.93450.02430.499926.858339.02948.1096
99.5909-0.1398-0.24113.974-0.37222.9759-0.0807-0.56080.05220.15070.02890.0544-0.1353-0.57130.09160.4608-0.0476-0.0040.5505-0.01530.324935.118952.44742.8335
109.61946.36193.71384.33042.80376.32860.2669-0.84132.02240.4362-0.3651.3839-1.0696-0.61770.08550.480.09380.04650.8316-0.08730.612426.535653.54449.4873
119.7034-0.0311-1.78339.47530.95075.4560.31070.15160.4551-0.0665-0.69110.8010.9332-1.31950.26270.4304-0.0932-0.11741.1068-0.00830.700420.454445.47916.1611
122.45350.39281.73018.41247.40897.5737-0.0835-0.1357-0.21740.0077-0.32160.11590.5395-0.76130.26850.7036-0.0473-0.1110.43320.00090.4955-5.024844.884411.6355
139.2276-4.0133-4.98863.21333.39053.76160.21410.53360.438-0.59010.5283-1.5672-0.15010.9474-0.87970.7045-0.0233-0.00350.72310.0040.55484.280943.87622.2042
144.90065.34233.9548.99630.3998.2603-0.3331-0.3294-1.42080.4967-0.3721-2.1710.89331.27960.58930.63940.1785-0.11550.79360.09430.80085.629832.36455.8418
156.8814-3.6454-1.60145.69056.47759.32840.0568-0.34860.3818-0.1810.10910.1154-0.4772-0.33160.02640.4768-0.0626-0.06910.31240.00610.4085-10.162444.77271.8629
166.14081.22020.98411.9672-0.03433.0415-0.2828-0.1831-0.3656-0.05250.1928-0.230.5345-0.02090.0920.61420.0383-0.03680.3953-0.03230.4106-10.872434.1227-1.5853
172.5834-3.67021.19136.295-4.23667.12280.0744-0.7971-1.2440.71820.11450.3350.9649-0.6029-0.23720.88980.0227-0.06660.51610.06640.5158-11.944429.75716.43
185.79761.26714.29891.69181.48273.5266-0.29931.5506-2.802-0.53610.6833-0.06882.83740.9524-0.29390.93650.0729-0.12370.6918-0.12830.733-3.621824.5714-1.9182
194.6988-0.4746-0.45681.83883.60557.5845-0.2882-0.7774-0.3772.4510.2558-1.48961.06921.0305-0.14611.19980.1761-0.30930.56770.09640.7199-0.073931.00758.8421
207.41121.30163.33213.75412.9933.16860.6983-0.2321-0.76650.64740.0142-0.19370.49410.1081-0.67290.6091-0.0076-0.09970.43450.07170.48150.727248.154813.9025
213.7496-0.49890.46781.37970.34563.38870.1701-0.4815-0.49120.1957-0.04960.10840.3998-0.4121-0.11930.5996-0.12130.01770.4572-0.00020.4128-11.736652.018520.3339
228.5172-0.9875-1.60398.41150.05886.25880.1634-0.47740.80470.07280.1138-0.0787-0.69770.2767-0.28460.4344-0.03770.06740.4163-0.04430.3791-7.143560.588715.5217
239.08275.765-0.64058.77440.1857.73240.984-0.3445-1.9504-1.1378-0.20730.5683-0.13880.6919-0.65470.60390.2619-0.00580.42160.03110.623243.488433.078844.2112
248.82-2.7448-3.46988.2333-1.9742.61680.2999-0.1446-1.43760.18890.021.09651.10170.4306-0.15552.59520.4632-0.51590.0780.14530.699140.574224.284136.636
253.91772.4493-5.94689.4734-5.69249.9662-0.95250.6727-1.8157-1.1045-0.0350.4260.4637-2.35620.85361.4184-0.4-0.32630.89840.0761.100430.087226.68238.7569
269.0703-1.25723.21673.74692.60483.88440.310.98590.2791-1.21480.5093-1.12390.76281.2141-0.8080.8674-0.00550.11460.77230.12590.796244.646238.93634.7567
277.43685.67571.65745.972.71781.53320.597-0.0617-1.2776-1.97310.02640.29952.0884-1.0073-0.38831.5368-0.4273-0.44370.65380.11440.813434.371734.251431.8347
287.0049-5.3109-0.37934.58060.78176.87510.31160.21440.2804-0.85020.26940.4097-0.6498-1.1887-0.56130.6752-0.0178-0.07070.52490.1330.464635.282850.697834.5886
298.4965.91283.46165.0644.80637.560.3148-1.6956-0.14531.41650.44492.12250.872-1.4352-0.70.6301-0.06790.03350.73230.33990.871830.73844.008441.6622
305.8726-4.37050.50587.3039-2.45916.38850.7899-0.3866-2.34690.01010.10952.49331.2071-1.1197-0.76530.5799-0.2289-0.22120.72340.20151.229726.019636.086836.9339
317.00881.79892.22677.452-4.23144.00740.29610.0243-0.3271.9589-0.0373-0.3067-1.2095-0.7642-0.28440.76450.0191-0.02380.4809-0.16680.59619.86977.205825.1896
325.30162.2532.12593.7567-2.38874.73691.02870.6338-1.1083-0.19590.7371-0.49211.09390.5818-1.50620.71970.0257-0.01620.5584-0.10790.705619.837267.379316.4056
339.01225.1457-4.51848.083-4.03368.08740.29420.54470.1050.9291-0.1296-0.3169-0.47-0.0515-0.11860.3792-0.05610.01590.34010.0170.307812.412171.496618.979
341.5912.04162.29487.95213.53288.0898-0.43190.4222-0.1555-0.65590.4405-1.2737-0.98570.8130.04550.437700.05960.4073-0.00480.540615.523779.540914.1468
353.537-1.9556-1.08727.5080.86124.25360.0539-0.12310.09850.642-0.11980.4862-0.0972-0.50160.10570.4934-0.07640.04820.5007-0.02110.37045.342481.715814.609
369.0903-0.86985.099.913-3.67253.90840.330.14020.2086-0.04610.07180.43590.706-0.0976-0.46320.5918-0.1080.09530.5175-0.03750.50443.017170.469916.5853
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 75 )A58 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 82 )A76 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 137 )A83 - 137
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 148 )A138 - 148
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 66 )B58 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 82 )B67 - 82
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 94 )B83 - 94
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 109 )B95 - 109
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 127 )B110 - 127
10X-RAY DIFFRACTION10chain 'B' and (resid 128 through 137 )B128 - 137
11X-RAY DIFFRACTION11chain 'B' and (resid 138 through 151 )B138 - 151
12X-RAY DIFFRACTION12chain 'C' and (resid 58 through 66 )C58 - 66
13X-RAY DIFFRACTION13chain 'C' and (resid 67 through 75 )C67 - 75
14X-RAY DIFFRACTION14chain 'C' and (resid 76 through 82 )C76 - 82
15X-RAY DIFFRACTION15chain 'C' and (resid 83 through 94 )C83 - 94
16X-RAY DIFFRACTION16chain 'C' and (resid 95 through 127 )C95 - 127
17X-RAY DIFFRACTION17chain 'C' and (resid 128 through 136 )C128 - 136
18X-RAY DIFFRACTION18chain 'C' and (resid 137 through 146 )C137 - 146
19X-RAY DIFFRACTION19chain 'C' and (resid 147 through 152 )C147 - 152
20X-RAY DIFFRACTION20chain 'D' and (resid 58 through 82 )D58 - 82
21X-RAY DIFFRACTION21chain 'D' and (resid 83 through 127 )D83 - 127
22X-RAY DIFFRACTION22chain 'D' and (resid 128 through 152 )D128 - 152
23X-RAY DIFFRACTION23chain 'E' and (resid 58 through 67 )E58 - 67
24X-RAY DIFFRACTION24chain 'E' and (resid 68 through 73 )E68 - 73
25X-RAY DIFFRACTION25chain 'E' and (resid 74 through 82 )E74 - 82
26X-RAY DIFFRACTION26chain 'E' and (resid 83 through 94 )E83 - 94
27X-RAY DIFFRACTION27chain 'E' and (resid 95 through 110 )E95 - 110
28X-RAY DIFFRACTION28chain 'E' and (resid 111 through 127 )E111 - 127
29X-RAY DIFFRACTION29chain 'E' and (resid 128 through 136 )E128 - 136
30X-RAY DIFFRACTION30chain 'E' and (resid 137 through 152 )E137 - 152
31X-RAY DIFFRACTION31chain 'F' and (resid 59 through 66 )F59 - 66
32X-RAY DIFFRACTION32chain 'F' and (resid 67 through 76 )F67 - 76
33X-RAY DIFFRACTION33chain 'F' and (resid 77 through 87 )F77 - 87
34X-RAY DIFFRACTION34chain 'F' and (resid 88 through 101 )F88 - 101
35X-RAY DIFFRACTION35chain 'F' and (resid 102 through 137 )F102 - 137
36X-RAY DIFFRACTION36chain 'F' and (resid 138 through 152 )F138 - 152

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万見について

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お知らせ

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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

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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

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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

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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

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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。

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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