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- PDB-9baj: Crystal structure of GDP-bound human K-RAS in a covalent complex ... -

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基本情報

登録情報
データベース: PDB / ID: 9baj
タイトルCrystal structure of GDP-bound human K-RAS in a covalent complex with aryl sulfonyl fluoride compounds.
要素(Isoform 2B of GTPase ...) x 3
キーワードHYDROLASE / KRAS / cancer / GTPase / covalent inhibitor / sulfonyl fluoride
機能・相同性
機能・相同性情報


forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / 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 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by CSF3 (G-CSF) / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / positive regulation of glial cell proliferation / FRS-mediated FGFR1 signaling / homeostasis of number of cells within a tissue / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / visual learning / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / RAS processing / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / MAPK cascade / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / G protein activity / actin cytoskeleton organization / Ca2+ pathway / RAF/MAP kinase cascade / neuron apoptotic process / gene expression / negative regulation of neuron apoptotic process / mitochondrial outer membrane / Ras protein signal transduction / Golgi membrane / focal adhesion / GTPase activity
類似検索 - 分子機能
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
: / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
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: 1.49 Å
データ登録者Landgraf, A.D. / Brenner, R.J. / Ghozayel, M.K. / Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA264471 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA197928 米国
引用ジャーナル: Chemmedchem / 年: 2025
タイトル: Small-Molecule KRAS Inhibitors by Tyrosine Covalent Bond Formation.
著者: Landgraf, A.D. / Brenner, R. / Ghozayel, M.K. / Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
履歴
登録2024年4月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年4月9日Provider: repository / タイプ: Initial release
改定 1.12025年6月11日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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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: Isoform 2B of GTPase KRas
B: Isoform 2B of GTPase KRas
C: Isoform 2B of GTPase KRas
D: Isoform 2B of GTPase KRas
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)80,11416
ポリマ－77,0554
非ポリマー3,05912
水13,926773
1
A: Isoform 2B of GTPase KRas
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0214
ポリマ－19,2561
非ポリマー7653
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Isoform 2B of GTPase KRas
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0374
ポリマ－19,2721
非ポリマー7653
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Isoform 2B of GTPase KRas
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0374
ポリマ－19,2721
非ポリマー7653
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Isoform 2B of GTPase KRas
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,0214
ポリマ－19,2561
非ポリマー7653
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)35.925, 83.827, 104.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

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Isoform 2B of GTPase ... , 3種, 4分子 ADBC

#1: タンパク質 Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


分子量: 19255.693 Da / 分子数: 2 / 変異: C118S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KRAS, KRAS2, RASK2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P01116, small monomeric GTPase
#2: タンパク質 Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


分子量: 19271.693 Da / 分子数: 1 / 変異: C118S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KRAS, KRAS2, RASK2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P01116, small monomeric GTPase
#3: タンパク質 Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


分子量: 19271.693 Da / 分子数: 1 / 変異: C118S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KRAS, KRAS2, RASK2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P01116, small monomeric GTPase

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非ポリマー , 4種, 785分子

#4: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mg
#5: 化合物
ChemComp-A1AK8 / 3-(dioxo-lambda~6~-sulfanyl)-N-phenylbenzene-1-sulfonamide


分子量: 297.350 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C12H11NO4S2 / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / コメント: GDP, エネルギー貯蔵分子*YM
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 773 / 由来タイプ: 天然 / 式: H2O

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詳細

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

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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: 2.06 Å3/Da / 溶媒含有率: 40.33 %
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: Ammonium chloride 0.2 M and PEG 3350 20%

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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: ALS / ビームライン: 4.2.2 / 波長: 1.0722 Å
検出器タイプ: RDI CMOS_8M / 検出器: CMOS / 日付: 2021年10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: 1.0722 Å / 相対比: 1
反射解像度: 1.49→44.43 Å / Num. obs: 100461 / % possible obs: 99.6 % / 冗長度: 3.5 % / Biso Wilson estimate: 16.16 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Rsym value: 0.07 / Net I/σ(I): 10.3
反射 シェル解像度: 1.49→1.52 Å / 冗長度: 3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4856 / CC1/2: 0.587 / Rpim(I) all: 0.538 / Rrim(I) all: 0.954 / Rsym value: 0.78 / % possible all: 97

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
Aimless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: 1.49→44.43 Å / SU ML: 0.1518 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 25.16
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2696 4764 4.92 %
Rwork0.2375 92084 -
obs0.239 96848 96.03 %
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 mean: 22.16 Å2
精密化ステップサイクル: LAST / 解像度: 1.49→44.43 Å
タンパク質核酸リガンド溶媒全体
原子数5424 0 80 773 6277
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00835620
X-RAY DIFFRACTIONf_angle_d0.98267617
X-RAY DIFFRACTIONf_chiral_restr0.0697836
X-RAY DIFFRACTIONf_plane_restr0.0103968
X-RAY DIFFRACTIONf_dihedral_angle_d13.3813798
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.32821860.30822977X-RAY DIFFRACTION94.73
1.51-1.530.31091560.28263116X-RAY DIFFRACTION99
1.53-1.550.26321520.2643196X-RAY DIFFRACTION99.14
1.55-1.560.24991820.263182X-RAY DIFFRACTION99.53
1.56-1.590.29631790.25583123X-RAY DIFFRACTION99.64
1.59-1.610.28721540.24523170X-RAY DIFFRACTION99.73
1.61-1.630.25921830.24253228X-RAY DIFFRACTION99.88
1.63-1.650.24931390.24333165X-RAY DIFFRACTION99.58
1.65-1.680.26621760.23633135X-RAY DIFFRACTION99.76
1.68-1.710.24851530.23353242X-RAY DIFFRACTION99.94
1.71-1.740.2691450.23593164X-RAY DIFFRACTION99.97
1.74-1.770.27921610.22873198X-RAY DIFFRACTION99.97
1.77-1.80.24631650.23923206X-RAY DIFFRACTION100
1.8-1.840.29061760.253149X-RAY DIFFRACTION100
1.84-1.870.31341290.28352486X-RAY DIFFRACTION98.46
1.88-1.920.4859820.52641588X-RAY DIFFRACTION55.04
1.92-1.970.4431790.32282660X-RAY DIFFRACTION84.54
1.97-2.020.24841490.21653197X-RAY DIFFRACTION99.97
2.02-2.080.22861560.21173226X-RAY DIFFRACTION99.88
2.08-2.150.2251600.21713170X-RAY DIFFRACTION99.91
2.15-2.230.31451480.32152996X-RAY DIFFRACTION92.74
2.23-2.320.47281540.41332852X-RAY DIFFRACTION90.22
2.32-2.420.25571530.20583227X-RAY DIFFRACTION99.91
2.42-2.550.26031610.22253194X-RAY DIFFRACTION99.79
2.55-2.710.21871670.2133195X-RAY DIFFRACTION99.85
2.71-2.920.22671700.21733208X-RAY DIFFRACTION99.68
2.92-3.210.25141610.19253198X-RAY DIFFRACTION99.88
3.21-3.680.2241510.20173234X-RAY DIFFRACTION99.53
3.68-4.630.21311570.1683193X-RAY DIFFRACTION98.59
4.63-44.430.2261800.19283209X-RAY DIFFRACTION98.09
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)
12.298325540521.072772639850.2416681850333.217552501561.754470240331.11463640072-0.08989061124860.06379039687330.300868806808-0.4012372154220.08280515537680.203883831358-0.285658707441-0.104574344973-0.0002795106643070.127938024870.004347681589060.007364696067190.1482447829970.01795140516760.0617385820709-8.65796264643-6.394686097199.65092591406
24.751352419540.191393820594-1.912278172390.937668617391-1.039033013931.84090907591-0.3980496773630.4039076979320.18989079495-0.3675718193050.2712840552660.1922910453660.30909678899-0.4431474938110.1584501051920.209239512158-0.0220056638519-0.01478258003310.257322701693-0.001282992195190.145205312502-11.352779971-16.00854079563.37828896386
34.21475601599-5.79486836804-2.297963951588.891039425022.508410973591.698257557740.2452818562790.2517489768610.066959576808-0.444822462796-0.3304354722550.116899539734-0.159049550511-0.09355897425560.0814614746540.123990791262-0.00440154062731-0.006207127679580.204704404522-0.03007906811410.139536463659-10.68825695681.245528959017.73565864829
40.7725080705570.504256560191-0.3766540625511.09434355133-0.2889792392390.70102635468-0.01249928104490.0499517980095-0.00544698851441-0.21143403925-0.0332441245373-0.131297003412-0.04976676042790.125025213890.04201164843450.1454813383014.71501120753E-50.005978681094070.1781877738610.009662615702170.1130216791461.33881516179-10.143170743711.21992229
54.507530396784.19841593407-0.2822086066417.30808066842-2.021389757472.39489214028-0.06087610341740.0381375886952-0.0508867161078-0.0487183238847-0.106849683389-0.4398379474910.01748514701190.3747535374340.1447676072520.0946453349120.00281836810105-0.01910216212030.2422964093620.02183257704110.1341070808863.25377387518-13.805327689320.1868491749
60.3505724042110.992654561916-0.5991256064793.12128189803-0.4847865939581.65439644119-0.016549500914-0.0932973229343-0.143329266561-0.0221488044141-0.0537052026045-0.219312924597-0.09250775421890.02733740291890.05732182859340.06662601595510.00111046944122-0.01783772020780.1370528916460.005388710003040.104571035558-7.50874274376-12.945360921121.8414461599
75.153028280281.04208992543.414408400191.695523042240.4347487993895.163353802460.0257911620277-0.169518667270.0749381284910.1540876538760.01176333216820.0835783979047-0.0572877613555-0.351019107153-0.04719009654690.09303573103080.01618842677620.02217278501550.1216417027890.001549268173850.0860313443843-10.7846619006-11.655779560924.6801037526
87.621290290115.00895888580.4594291433258.850162375361.604783687835.1405325739-0.0123141479763-0.1157993763930.2695307386680.3366356554820.233868345202-0.05061509223-0.1717610303090.453838471633-0.1540048561530.1075152331430.04126838164720.007456930372210.151816120243-0.0240431223080.118709124667-9.356241846531.453592086918.4402555268
92.02747269644-0.4196266942320.5936403379274.127459348720.9161142952560.843829500044-0.071298816734-0.0627273239574-0.172307377320.4734882232950.08961271185570.07081273021840.0758427989682-0.185424575163-0.01472476111680.145170064227-0.0160022751161-0.00416948103110.1803157429080.02286482982090.06505258384433.870540298528.2135796221743.587275334
103.54035065669-1.50033356053.027927523661.05512310963-1.056217285342.74792604128-0.481425080352-0.2546456532450.1139932617710.539918289160.2121055262660.0325051783129-0.314920608538-0.3257776499160.1922516101640.179457308614-0.0132800202425-0.04726360915030.218265787326-0.02834396733960.1415228622034.3797791073818.56488019949.0242493736
117.124188276883.841844317033.657304322654.594117089481.655035117844.458005867760.174988941794-0.559706315606-0.2792787204040.184182671911-0.02679280465290.6663879087870.0767009488491-0.528276213001-0.1124379865620.1471110073840.00332558225773-0.05419952624860.2132114090810.06118377141470.265459650427-0.1471102690591.5162001748345.7316303597
125.796888084110.9179480112413.752826927084.908950116582.668143289633.48652980975-0.05239152509520.260616597224-0.0983332857193-0.0777049812150.171533984872-0.2960427624610.1549349161970.369427091806-0.1228375645310.1540919100350.05611620717360.009353795937810.220711922742-0.0067165556550.096859858555418.43163651076.5592677856746.0843120802
131.73878101027-1.36040035853-0.242556967988.79207049413-2.775184036893.506154675390.08295798075030.2944569735980.118255721499-0.0775817560046-0.156381697928-0.391037618357-0.2167125447590.1902199366220.04068474103970.0914905870614-0.00618528304127-0.008477819407840.170849214371-0.00759391877640.08481007700910.763498518514.837443237633.5481354945
142.54652043661-2.448515510441.518700923036.223409841510.6574483022642.12283584924-0.176264709685-0.2946880898940.0106690082728-0.4888722576580.0220509535848-0.932011167063-0.2533939460380.6223309934250.1423186168310.04480641324920.03118510370330.01938234235770.3902064483650.002210890909670.29705105313719.02846783947.4030334645733.792943963
151.97742764953-0.106362835050.5755119001273.44951175555-0.6974047950422.572469501320.1308673193330.342947798342-0.0552500359623-0.541188938847-0.175789356934-0.14805205369-0.04738696900060.1973803349170.07610331721380.11174685481-0.02581628330570.0004420627521530.198497295532-0.0009733997142940.07510274405027.1950360777913.239653957431.1375413969
162.69517278722-2.19230400141-1.243445916574.915088820012.453191477335.121162872220.09668465935380.2961338460470.0480363021232-0.299592060733-0.0358671363277-0.0299789981056-0.211243348779-0.0420922132662-0.03706101272390.120384169038-0.0246831319865-0.01624052025340.194553351336-0.007239563061920.09799097894583.5380504034412.678010419128.2837062361
170.4907427440381.047345199881.257231873158.464550870131.957730030514.36732755193-0.004560694126870.0254109100194-0.1285131067570.0503578338941-0.001275261248260.1921883606850.201464262677-0.233376056626-0.04129573002530.0544176547349-0.0310919941283-0.01102605364990.1627814014840.005474661342280.1186306515540.8827664934441.2939619054335.0668685322
182.13665671718-1.03796836676-0.1935828014394.391189142981.814643989140.85079672228-0.0992949889118-0.0384217615561-0.2327031663530.3874565335040.1148148371750.2137392603250.17230720447-0.122808219447-0.005604950281120.118339198121-0.0051704155847-0.008580276473630.1577315564260.02062789803470.05188539068949.295485272847.33327613742.7511131124
194.829737817320.254817948321.651801344181.29007554029-0.9236409572451.73112963585-0.208815432062-0.440955979635-0.05913341948420.5274118565190.1423531125990.167026607917-0.205795573958-0.3996410166580.09621301893280.2131749731440.03178489432360.01446985725590.249788270188-0.008979934512610.1333224270786.6049151278256.933698615149.0133023065
203.793558254665.583828344882.219793187339.030727937772.580339349791.819101395880.122986352951-0.138132303487-0.04188320845950.338679328219-0.1855685877650.1253194917820.0812931525587-0.06286991580210.06244915968250.10958637480.008925695555970.01012316812110.197405234144-0.02214131779970.1329917450247.2681375260639.661327598544.6153939514
211.75893775997-0.475546723621.036009857030.8053862022080.1244500902521.45108335107-0.03227845964060.0404631539972-0.00237694185150.2087201260060.0188043720133-0.1400116335470.08015978486770.2661603134820.006183823699360.1431654391060.00362163026682-0.00956093039840.1855083744710.01353152651550.10649259560820.652154689649.619853757942.2067152597
223.45283570008-3.06566564468-0.9231351950355.207791184470.8281217405987.179298886180.1534159447820.1537999549510.611289072544-0.248386319796-0.111967733407-0.350131182546-0.4287472608130.366213154033-0.08551695238760.1130170314474.11820941212E-50.01225699695840.1273732680350.009590302184650.094732082203313.052329183462.932440413631.0386505309
234.10038881486-4.426930370291.392306054566.57955320797-2.792093868052.786822101630.0717910366899-0.215745329454-0.2508213639580.10221850935-0.209384925486-0.1189324448580.1495316749730.5322567010730.1624033905140.1336763414890.01685086555580.0222127368290.2665469536690.04264233639180.18420472244123.698309057251.214898603333.0004638121
240.4865442060310.1218883807431.064838939951.94637220723-0.6254576921742.7457524980.09952746384460.135619060990.127341074076-0.103519899098-0.117371182262-0.4898160252540.2087716518870.231055665806-0.01877819891630.1144766415240.02057416503740.02467667556040.1406059438990.007497643765080.14850708183917.024511048546.116980379130.9578756075
251.97999578841-0.0931159704272-0.7049800184273.00940385311-2.692062882725.07432228891-0.2166868262910.05307947011510.234839765631-0.007343775815240.167306052956-0.00724365438258-0.0483792844026-0.2684223146110.06123103369610.06927354329360.023428077063-0.01259751045630.151978161930.0004381126789360.149057989092.937933145762.8019561530.1380781632
264.83537360179-0.964225991049-3.109349266061.877241497730.4604527996275.08180261793-0.02888688335020.251030503837-0.0439386195668-0.1733967020340.01481081840170.08856219208170.0614014455304-0.3785119999640.004554893310590.103348742769-0.0189643022277-0.02016629302480.120965620107-0.0007477960453160.08203653792877.1841574478852.599456526227.7247984029
278.96434935678-5.09053725826-0.4378177928695.516930644561.942177248346.096557413610.095289532518-0.0227222509485-0.295915506723-0.1477277015330.08865000812440.03041847442190.2907767267810.329156066996-0.1437451399290.10758895045-0.0484337987629-0.01440654082350.1418388936730.003458173429880.134721800178.6303750944539.478546831833.9670548123
282.302971451720.1428037297-0.6946988269043.936609367431.148157431891.20046001101-0.03558616493370.07996690093590.165472951104-0.4529294173480.1042906597240.121798148429-0.100328631507-0.228468029478-0.0565346598440.1437887377360.005679085532350.0008034737357560.1741574641340.03351037063440.06577667848221.855826258232.75418564798.81922830703
293.31003827671.1786776658-2.796001153621.13160544771-0.7569453417222.53441611203-0.441867949085-0.0346540105509-0.234145415764-0.5629956462510.1046457048060.07574477397530.380165154617-0.2236707733960.2871024462860.180868597367-0.01162591493710.05742083467050.233254087167-0.02560567291570.15104492302522.322403264422.40887175823.3481839035
305.34405425457-1.57639981103-2.827740008693.660253460770.7575039734552.499858277740.02118852367010.0806866005030.1262210630660.01302588318180.1025568658280.130724128805-0.1772423623950.0242809788873-0.1333066075340.174973943455-0.02438011901230.02964651465330.1449430577530.0159080261620.068856475098326.585016744637.06402600596.53189951148
311.789427077710.4955294677830.2939322643063.93500973258-0.2804224533241.7999873380.0428161529902-0.246425942216-0.008541992395360.288074443823-0.0626567099873-0.4484993844020.06475013565410.2728421322330.03087567904980.09861728249210.01043261107930.003668778549190.19758934743-0.01802219603790.12138233482929.679301001928.798565752319.7092479435
322.590877770442.440345249021.445580594434.944204134332.633775885885.37428716520.202317166364-0.190483908209-0.02874308432870.459610090845-0.118577192282-0.001434817395220.422429566241-0.0657923419508-0.05026157605010.1300798710590.01889525461750.01560872495660.189790620041-0.00795631492820.11400318384121.367317551228.207709275424.1182087295
331.77342407053-1.2904606188-2.229828771588.330549264071.567497221035.326967891860.04090261710760.03659282776030.193953738590.07122272610120.0834108433580.135653515329-0.224321065084-0.172636296769-0.1136460996660.06291015926210.0252257570760.02031335858030.157078718471-0.003239469268470.113077304118.834270666739.650746088117.337536068
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 'A' and (resid 1 through 25 )AA1 - 251 - 25
22chain 'A' and (resid 26 through 37 )AA26 - 3726 - 37
33chain 'A' and (resid 38 through 57 )AA38 - 5738 - 57
44chain 'A' and (resid 58 through 86 )AA58 - 8658 - 86
55chain 'A' and (resid 87 through 104 )AA87 - 10487 - 104
66chain 'A' and (resid 105 through 126 )AA105 - 126105 - 126
77chain 'A' and (resid 127 through 151 )AA127 - 151127 - 151
88chain 'A' and (resid 152 through 167 )AA152 - 167152 - 167
99chain 'B' and (resid 1 through 25 )BD1 - 251 - 25
1010chain 'B' and (resid 26 through 37 )BD26 - 3726 - 37
1111chain 'B' and (resid 38 through 57 )BD38 - 5738 - 57
1212chain 'B' and (resid 58 through 74 )BD58 - 7458 - 74
1313chain 'B' and (resid 75 through 92 )BD75 - 9275 - 92
1414chain 'B' and (resid 93 through 104 )BD93 - 10493 - 104
1515chain 'B' and (resid 105 through 126 )BD105 - 126105 - 126
1616chain 'B' and (resid 127 through 151 )BD127 - 151127 - 151
1717chain 'B' and (resid 152 through 166 )BD152 - 166152 - 166
1818chain 'C' and (resid 1 through 25 )CG1 - 251 - 25
1919chain 'C' and (resid 26 through 37 )CG26 - 3726 - 37
2020chain 'C' and (resid 38 through 57 )CG38 - 5738 - 57
2121chain 'C' and (resid 58 through 83 )CG58 - 8358 - 83
2222chain 'C' and (resid 84 through 92 )CG84 - 9284 - 92
2323chain 'C' and (resid 93 through 104 )CG93 - 10493 - 104
2424chain 'C' and (resid 105 through 116 )CG105 - 116105 - 116
2525chain 'C' and (resid 117 through 126 )CG117 - 126117 - 126
2626chain 'C' and (resid 127 through 151 )CG127 - 151127 - 151
2727chain 'C' and (resid 152 through 167 )CG152 - 167152 - 167
2828chain 'D' and (resid 1 through 25 )DJ1 - 251 - 25
2929chain 'D' and (resid 26 through 37 )DJ26 - 3726 - 37
3030chain 'D' and (resid 38 through 74 )DJ38 - 7438 - 74
3131chain 'D' and (resid 75 through 126 )DJ75 - 12675 - 126
3232chain 'D' and (resid 127 through 151 )DJ127 - 151127 - 151
3333chain 'D' and (resid 152 through 166 )DJ152 - 166152 - 166

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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