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- PDB-8pyi: Human IGF1R with inhibitor 6 -

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基本情報

登録情報
データベース: PDB / ID: 8pyi
タイトルHuman IGF1R with inhibitor 6
要素Insulin-like growth factor 1 receptor beta chain
キーワードTRANSFERASE / Tyrosine / Kinase
機能・相同性
機能・相同性情報


cardiac atrium development / negative regulation of cholangiocyte apoptotic process / positive regulation of steroid hormone biosynthetic process / protein kinase complex / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / IRS-related events triggered by IGF1R / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / positive regulation of steroid hormone biosynthetic process / protein kinase complex / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / IRS-related events triggered by IGF1R / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / cellular response to testosterone stimulus / insulin receptor complex / transcytosis / insulin-like growth factor I binding / negative regulation of hepatocyte apoptotic process / positive regulation of protein-containing complex disassembly / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / regulation of JNK cascade / dendritic spine maintenance / insulin binding / cellular response to insulin-like growth factor stimulus / response to L-glutamate / establishment of cell polarity / positive regulation of axon regeneration / positive regulation of osteoblast proliferation / positive regulation of cytokinesis / amyloid-beta clearance / Respiratory syncytial virus (RSV) attachment and entry / insulin receptor substrate binding / cellular response to angiotensin / response to vitamin E / G-protein alpha-subunit binding / negative regulation of MAPK cascade / phosphatidylinositol 3-kinase binding / SHC-related events triggered by IGF1R / peptidyl-tyrosine autophosphorylation / estrous cycle / cellular response to transforming growth factor beta stimulus / T-tubule / cerebellum development / cellular response to dexamethasone stimulus / axonogenesis / insulin-like growth factor receptor signaling pathway / hippocampus development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to nicotine / positive regulation of smooth muscle cell proliferation / insulin receptor binding / cellular response to estradiol stimulus / placental growth factor receptor activity / cellular response to glucose stimulus / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / caveola / cellular response to mechanical stimulus / cellular response to amyloid-beta / cellular senescence / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein autophosphorylation / protein tyrosine kinase activity / response to ethanol / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / immune response / cilium / positive regulation of cell migration / axon / neuronal cell body / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / signal transduction / ATP binding / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats ...Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Chem-IER / Insulin-like growth factor 1 receptor
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: 3.06 Å
データ登録者Dreyer, M.K. / Wang, J. / Elkins, J.M.
資金援助 スイス, 1件
組織認可番号国
Innovative Medicines InitiativeK4DD スイス
引用ジャーナル: To Be Published
タイトル: Human IGF1R with inhibitor 6
著者: Dreyer, M.K. / Wang, J. / Elkins, J.M.
履歴
登録2023年7月25日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年9月20日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
AAA: Insulin-like growth factor 1 receptor beta chain
BBB: Insulin-like growth factor 1 receptor beta chain
CCC: Insulin-like growth factor 1 receptor beta chain
DDD: Insulin-like growth factor 1 receptor beta chain
EEE: Insulin-like growth factor 1 receptor beta chain
FFF: Insulin-like growth factor 1 receptor beta chain
GGG: Insulin-like growth factor 1 receptor beta chain
HHH: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)297,59616
ポリマ－293,7288
非ポリマー3,8688
水3,135174
1
AAA: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,2002
ポリマ－36,7161
非ポリマー4841
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
BBB: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,2002
ポリマ－36,7161
非ポリマー4841
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
CCC: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,2002
ポリマ－36,7161
非ポリマー4841
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
DDD: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,2002
ポリマ－36,7161
非ポリマー4841
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
EEE: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,2002
ポリマ－36,7161
非ポリマー4841
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
FFF: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,2002
ポリマ－36,7161
非ポリマー4841
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
GGG: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,2002
ポリマ－36,7161
非ポリマー4841
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
HHH: Insulin-like growth factor 1 receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,2002
ポリマ－36,7161
非ポリマー4841
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)128.586, 103.948, 191.816
Angle α, β, γ (deg.)90.000, 100.170, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74AAA
84EEE
95AAA
105FFF
116AAA
126GGG
137AAA
147HHH
158BBB
168CCC
179BBB
189DDD
1910BBB
2010EEE
2111BBB
2211FFF
2312BBB
2412GGG
2513BBB
2613HHH
2714CCC
2814DDD
2915CCC
3015EEE
3116CCC
3216FFF
3317CCC
3417GGG
3518CCC
3618HHH
3719DDD
3819EEE
3920DDD
4020FFF
4121DDD
4221GGG
4322DDD
4422HHH
4523EEE
4623FFF
4724EEE
4824GGG
4925EEE
5025HHH
5126FFF
5226GGG
5327FFF
5427HHH
5528GGG
5628HHH

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
111VALVALGLUGLUAAAA986 - 128414 - 312
221VALVALGLUGLUBBBB986 - 128414 - 312
332TYRTYRGLUGLUAAAA987 - 128415 - 312
442TYRTYRGLUGLUCCCC987 - 128415 - 312
553TYRTYRGLUGLUAAAA987 - 128415 - 312
663TYRTYRGLUGLUDDDD987 - 128415 - 312
774TYRTYRGLUGLUAAAA987 - 128415 - 312
884TYRTYRGLUGLUEEEE987 - 128415 - 312
995TYRTYRASNASNAAAA987 - 128515 - 313
10105TYRTYRASNASNFFFF987 - 128515 - 313
11116TYRTYRASNASNAAAA987 - 128515 - 313
12126TYRTYRASNASNGGGG987 - 128515 - 313
13137TYRTYRGLUGLUAAAA987 - 128415 - 312
14147TYRTYRGLUGLUHHHH987 - 128415 - 312
15158TYRTYRGLUGLUBBBB987 - 128415 - 312
16168TYRTYRGLUGLUCCCC987 - 128415 - 312
17179TYRTYRASNASNBBBB987 - 128515 - 313
18189TYRTYRASNASNDDDD987 - 128515 - 313
191910TYRTYRASNASNBBBB987 - 128515 - 313
202010TYRTYRASNASNEEEE987 - 128515 - 313
212111TYRTYRASNASNBBBB987 - 128515 - 313
222211TYRTYRASNASNFFFF987 - 128515 - 313
232312TYRTYRASNASNBBBB987 - 128515 - 313
242412TYRTYRASNASNGGGG987 - 128515 - 313
252513TYRTYRASNASNBBBB987 - 128515 - 313
262613TYRTYRASNASNHHHH987 - 128515 - 313
272714TYRTYRASNASNCCCC987 - 128515 - 313
282814TYRTYRASNASNDDDD987 - 128515 - 313
292915TYRTYRASNASNCCCC987 - 128515 - 313
303015TYRTYRASNASNEEEE987 - 128515 - 313
313116TYRTYRASNASNCCCC987 - 128515 - 313
323216TYRTYRASNASNFFFF987 - 128515 - 313
333317TYRTYRASNASNCCCC987 - 128515 - 313
343417TYRTYRASNASNGGGG987 - 128515 - 313
353518TYRTYRASNASNCCCC987 - 128515 - 313
363618TYRTYRASNASNHHHH987 - 128515 - 313
373719TYRTYRASNASNDDDD987 - 128515 - 313
383819TYRTYRASNASNEEEE987 - 128515 - 313
393920TYRTYRASNASNDDDD987 - 128515 - 313
404020TYRTYRASNASNFFFF987 - 128515 - 313
414121TYRTYRASNASNDDDD987 - 128515 - 313
424221TYRTYRASNASNGGGG987 - 128515 - 313
434322TYRTYRASNASNDDDD987 - 128515 - 313
444422TYRTYRASNASNHHHH987 - 128515 - 313
454523TYRTYRASNASNEEEE987 - 128515 - 313
464623TYRTYRASNASNFFFF987 - 128515 - 313
474724TYRTYRASNASNEEEE987 - 128515 - 313
484824TYRTYRASNASNGGGG987 - 128515 - 313
494925TYRTYRASNASNEEEE987 - 128515 - 313
505025TYRTYRASNASNHHHH987 - 128515 - 313
515126TYRTYRASNASNFFFF987 - 128515 - 313
525226TYRTYRASNASNGGGG987 - 128515 - 313
535327TYRTYRASNASNFFFF987 - 128515 - 313
545427TYRTYRASNASNHHHH987 - 128515 - 313
555528TYRTYRASNASNGGGG987 - 128515 - 313
565628TYRTYRASNASNHHHH987 - 128515 - 313

NCSアンサンブル:
ID詳細
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

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要素

#1: タンパク質
Insulin-like growth factor 1 receptor beta chain


分子量: 36715.988 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IGF1R / プラスミド: pFB-CT10HF-LIC / 細胞株 (発現宿主): Sf9
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P08069
#2: 化合物
ChemComp-IER / 3-[8-azanyl-1-(4-ethoxy-8-fluoranyl-2-phenyl-quinolin-7-yl)imidazo[1,5-a]pyrazin-3-yl]-1-methyl-cyclobutan-1-ol / A156


分子量: 483.537 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C28H26FN5O2 / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 174 / 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: 2.15 Å3/Da / 溶媒含有率: 42.73 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / 詳細: 0.1 M Bis-Tris, 0.3 M MgCl2, 20% PEG 3350

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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: SLS / ビームライン: X10SA / 波長: 0.99997 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2014年8月21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: 0.99997 Å / 相対比: 1
反射解像度: 3.057→71.103 Å / Num. obs: 47077 / % possible obs: 99.6 % / 冗長度: 3.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.3
反射 シェル解像度: 3.057→3.067 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 482

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0267精密化
XDSデータ削減
SCALA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: 3.06→63.474 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 22.85 / SU ML: 0.385 / 交差検証法: FREE R-VALUE / ESU R Free: 0.477 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射
Rfree0.2352 2372 5.055 %
Rwork0.1911 44556 -
all0.193 --
obs-46928 99.616 %
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータBiso mean: 55.063 Å2
Baniso -1Baniso -2Baniso -3
1-6.378 Å2-0 Å2-1.03 Å2
2---2.031 Å20 Å2
3----3.737 Å2
精密化ステップサイクル: LAST / 解像度: 3.06→63.474 Å
タンパク質核酸リガンド溶媒全体
原子数18398 0 288 174 18860
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01319117
X-RAY DIFFRACTIONr_bond_other_d0.0010.01517912
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.67225836
X-RAY DIFFRACTIONr_angle_other_deg1.1861.58541063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00452265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87622.0231038
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.882153382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.815141
X-RAY DIFFRACTIONr_chiral_restr0.0580.22342
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221239
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024363
X-RAY DIFFRACTIONr_nbd_refined0.1980.23979
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.217127
X-RAY DIFFRACTIONr_nbtor_refined0.1690.29117
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.29564
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2357
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1960.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5420.2123
X-RAY DIFFRACTIONr_nbd_other0.4390.2247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5980.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3950.22
X-RAY DIFFRACTIONr_mcbond_it4.9765.5419132
X-RAY DIFFRACTIONr_mcbond_other4.9725.5419131
X-RAY DIFFRACTIONr_mcangle_it8.0338.30211373
X-RAY DIFFRACTIONr_mcangle_other8.0348.30311374
X-RAY DIFFRACTIONr_scbond_it5.4546.0669984
X-RAY DIFFRACTIONr_scbond_other5.4546.0669985
X-RAY DIFFRACTIONr_scangle_it8.9328.87714447
X-RAY DIFFRACTIONr_scangle_other8.9328.87714447
X-RAY DIFFRACTIONr_lrange_it12.38361.78821567
X-RAY DIFFRACTIONr_lrange_other12.38261.79621562
X-RAY DIFFRACTIONr_ncsr_local_group_10.0410.059338
X-RAY DIFFRACTIONr_ncsr_local_group_20.0370.059297
X-RAY DIFFRACTIONr_ncsr_local_group_30.0380.059336
X-RAY DIFFRACTIONr_ncsr_local_group_40.0360.059307
X-RAY DIFFRACTIONr_ncsr_local_group_50.0350.059356
X-RAY DIFFRACTIONr_ncsr_local_group_60.040.059316
X-RAY DIFFRACTIONr_ncsr_local_group_70.0370.059303
X-RAY DIFFRACTIONr_ncsr_local_group_80.0240.059397
X-RAY DIFFRACTIONr_ncsr_local_group_90.0210.059473
X-RAY DIFFRACTIONr_ncsr_local_group_100.0250.059432
X-RAY DIFFRACTIONr_ncsr_local_group_110.0220.059431
X-RAY DIFFRACTIONr_ncsr_local_group_120.0230.059420
X-RAY DIFFRACTIONr_ncsr_local_group_130.0210.059443
X-RAY DIFFRACTIONr_ncsr_local_group_140.0230.059449
X-RAY DIFFRACTIONr_ncsr_local_group_150.0290.059416
X-RAY DIFFRACTIONr_ncsr_local_group_160.0260.059390
X-RAY DIFFRACTIONr_ncsr_local_group_170.0260.059416
X-RAY DIFFRACTIONr_ncsr_local_group_180.0230.059401
X-RAY DIFFRACTIONr_ncsr_local_group_190.0240.059434
X-RAY DIFFRACTIONr_ncsr_local_group_200.0260.059430
X-RAY DIFFRACTIONr_ncsr_local_group_210.0220.059431
X-RAY DIFFRACTIONr_ncsr_local_group_220.0210.059441
X-RAY DIFFRACTIONr_ncsr_local_group_230.0190.059406
X-RAY DIFFRACTIONr_ncsr_local_group_240.0250.059417
X-RAY DIFFRACTIONr_ncsr_local_group_250.0170.059404
X-RAY DIFFRACTIONr_ncsr_local_group_260.0270.059379
X-RAY DIFFRACTIONr_ncsr_local_group_270.0260.059436
X-RAY DIFFRACTIONr_ncsr_local_group_280.0230.059403
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.040670.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.040670.0501
23AAAX-RAY DIFFRACTIONLocal ncs0.03720.0501
24CCCX-RAY DIFFRACTIONLocal ncs0.03720.0501
35AAAX-RAY DIFFRACTIONLocal ncs0.038080.0501
36DDDX-RAY DIFFRACTIONLocal ncs0.038080.0501
47AAAX-RAY DIFFRACTIONLocal ncs0.036440.0501
48EEEX-RAY DIFFRACTIONLocal ncs0.036440.0501
59AAAX-RAY DIFFRACTIONLocal ncs0.0350.0501
510FFFX-RAY DIFFRACTIONLocal ncs0.0350.0501
611AAAX-RAY DIFFRACTIONLocal ncs0.04040.0501
612GGGX-RAY DIFFRACTIONLocal ncs0.04040.0501
713AAAX-RAY DIFFRACTIONLocal ncs0.037360.0501
714HHHX-RAY DIFFRACTIONLocal ncs0.037360.0501
815BBBX-RAY DIFFRACTIONLocal ncs0.023510.0501
816CCCX-RAY DIFFRACTIONLocal ncs0.023510.0501
917BBBX-RAY DIFFRACTIONLocal ncs0.021280.0501
918DDDX-RAY DIFFRACTIONLocal ncs0.021280.0501
1019BBBX-RAY DIFFRACTIONLocal ncs0.024990.0501
1020EEEX-RAY DIFFRACTIONLocal ncs0.024990.0501
1121BBBX-RAY DIFFRACTIONLocal ncs0.021650.0501
1122FFFX-RAY DIFFRACTIONLocal ncs0.021650.0501
1223BBBX-RAY DIFFRACTIONLocal ncs0.02270.0501
1224GGGX-RAY DIFFRACTIONLocal ncs0.02270.0501
1325BBBX-RAY DIFFRACTIONLocal ncs0.020550.0501
1326HHHX-RAY DIFFRACTIONLocal ncs0.020550.0501
1427CCCX-RAY DIFFRACTIONLocal ncs0.023450.0501
1428DDDX-RAY DIFFRACTIONLocal ncs0.023450.0501
1529CCCX-RAY DIFFRACTIONLocal ncs0.029260.0501
1530EEEX-RAY DIFFRACTIONLocal ncs0.029260.0501
1631CCCX-RAY DIFFRACTIONLocal ncs0.025770.0501
1632FFFX-RAY DIFFRACTIONLocal ncs0.025770.0501
1733CCCX-RAY DIFFRACTIONLocal ncs0.026270.0501
1734GGGX-RAY DIFFRACTIONLocal ncs0.026270.0501
1835CCCX-RAY DIFFRACTIONLocal ncs0.023270.0501
1836HHHX-RAY DIFFRACTIONLocal ncs0.023270.0501
1937DDDX-RAY DIFFRACTIONLocal ncs0.024380.0501
1938EEEX-RAY DIFFRACTIONLocal ncs0.024380.0501
2039DDDX-RAY DIFFRACTIONLocal ncs0.026080.0501
2040FFFX-RAY DIFFRACTIONLocal ncs0.026080.0501
2141DDDX-RAY DIFFRACTIONLocal ncs0.021840.0501
2142GGGX-RAY DIFFRACTIONLocal ncs0.021840.0501
2243DDDX-RAY DIFFRACTIONLocal ncs0.020930.0501
2244HHHX-RAY DIFFRACTIONLocal ncs0.020930.0501
2345EEEX-RAY DIFFRACTIONLocal ncs0.019190.0501
2346FFFX-RAY DIFFRACTIONLocal ncs0.019190.0501
2447EEEX-RAY DIFFRACTIONLocal ncs0.024760.0501
2448GGGX-RAY DIFFRACTIONLocal ncs0.024760.0501
2549EEEX-RAY DIFFRACTIONLocal ncs0.017030.0501
2550HHHX-RAY DIFFRACTIONLocal ncs0.017030.0501
2651FFFX-RAY DIFFRACTIONLocal ncs0.027190.0501
2652GGGX-RAY DIFFRACTIONLocal ncs0.027190.0501
2753FFFX-RAY DIFFRACTIONLocal ncs0.025750.0501
2754HHHX-RAY DIFFRACTIONLocal ncs0.025750.0501
2855GGGX-RAY DIFFRACTIONLocal ncs0.022980.0501
2856HHHX-RAY DIFFRACTIONLocal ncs0.022980.0501
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.06-3.1390.3211710.28632440.28834210.7910.80199.82460.276
3.139-3.2250.3361650.27332040.27633750.7620.79599.82220.259
3.225-3.3180.2731690.24631150.24732910.8450.8699.78730.228
3.318-3.420.2961560.24130040.24431740.8450.8799.55890.221
3.42-3.5320.2431660.20128910.20430670.9080.91299.6740.183
3.532-3.6560.2481560.228390.20230030.9030.91899.73360.18
3.656-3.7930.2421470.18927270.19128840.9110.92999.65330.17
3.793-3.9470.2511390.19226450.19527970.9170.93199.53520.171
3.947-4.1220.2081300.16525500.16726880.940.95199.70240.148
4.122-4.3220.211270.14924040.15225360.940.95999.80280.135
4.322-4.5550.181070.1523260.15124360.9550.96299.87680.135
4.555-4.830.1981230.14821660.1522960.9450.96199.69510.132
4.83-5.1610.228980.1720770.17321830.9340.95299.63350.151
5.161-5.5720.2491060.19318910.19620070.920.93999.50170.174
5.572-6.0990.2181130.18717460.18918630.9390.9599.78530.168
6.099-6.8110.212830.19616090.19716960.9420.93799.76420.181
6.811-7.8490.21770.17214060.17414910.9470.95499.46340.16
7.849-9.5770.167600.15312210.15412880.9780.97699.45650.152
9.577-13.3920.168480.1749520.17410110.9720.97298.9120.18
13.392-63.4740.385310.2875400.2925970.8710.89695.64490.291

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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