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- PDB-8v8j: PI3Ka H1047R co-crystal structure with inhibitors in two cryptic ... -

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基本情報

登録情報
データベース: PDB / ID: 8v8j
タイトルPI3Ka H1047R co-crystal structure with inhibitors in two cryptic pockets (compounds 4 and 5).
要素
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
キーワードSIGNALING PROTEIN / H1047R / PI3K / PI3Ka
機能・相同性
機能・相同性情報


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / negative regulation of actin filament depolymerization / phosphatidylinositol kinase activity / response to L-leucine / regulation of actin filament organization / response to butyrate / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / negative regulation of actin filament depolymerization / phosphatidylinositol kinase activity / response to L-leucine / regulation of actin filament organization / response to butyrate / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / interleukin-18-mediated signaling pathway / myeloid leukocyte migration / autosome genomic imprinting / phosphatidylinositol 3-kinase complex / T follicular helper cell differentiation / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of cellular respiration / neurotrophin TRKA receptor binding / positive regulation of protein localization to membrane / Activated NTRK2 signals through PI3K / cis-Golgi network / negative regulation of fibroblast apoptotic process / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / phosphatidylinositol 3-kinase complex, class IB / vasculature development / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / cardiac muscle cell contraction / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / kinase activator activity / Nephrin family interactions / anoikis / Signaling by LTK in cancer / phosphatidylinositol-3-phosphate biosynthetic process / positive regulation of leukocyte migration / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / negative regulation of stress fiber assembly / RND1 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / positive regulation of filopodium assembly / RND2 GTPase cycle / phosphatidylinositol 3-kinase / vascular endothelial growth factor signaling pathway / RND3 GTPase cycle / relaxation of cardiac muscle / insulin binding / growth hormone receptor signaling pathway / 1-phosphatidylinositol-3-kinase activity / Signaling by ALK / RHOV GTPase cycle / PI-3K cascade:FGFR3 / RHOB GTPase cycle / natural killer cell mediated cytotoxicity / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / negative regulation of macroautophagy / GP1b-IX-V activation signalling / PI-3K cascade:FGFR2 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / negative regulation of osteoclast differentiation / Synthesis of PIPs at the plasma membrane / response to dexamethasone / RHOU GTPase cycle / CDC42 GTPase cycle / negative regulation of anoikis / RET signaling / PI3K events in ERBB2 signaling / protein kinase activator activity / insulin receptor substrate binding / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOG GTPase cycle / regulation of multicellular organism growth / intercalated disc / negative regulation of cell-matrix adhesion / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / positive regulation of TOR signaling / RAC2 GTPase cycle
類似検索 - 分子機能
PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain ...PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Rho GTPase activation protein / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
: / : / : / Phosphatidylinositol 3-kinase regulatory subunit alpha / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
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: 3.35 Å
データ登録者Gunn, R.J. / Lawson, J.D.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: J.Med.Chem. / 年: 2024
タイトル: Discovery of Pyridopyrimidinones that Selectively Inhibit the H1047R PI3K alpha Mutant Protein.
著者: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / ...著者: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / Gunn, R.J. / Ivetac, A. / Jones, B. / Kuehler, J. / Lawson, J.D. / Nguyen, N. / Parker, C. / Pearson, K.E. / Rahbaek, L. / Saechao, B. / Wang, X. / Waters, A. / Waters, L. / Watkins, A.H. / Olson, P. / Smith, C.R. / Christensen, J.G. / Marx, M.A.
履歴
登録2023年12月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年3月20日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22024年4月10日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)319,57810
ポリマ－316,9554
非ポリマー2,6236
水00
1
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)159,7895
ポリマ－158,4772
非ポリマー1,3123
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-14 kcal/mol
Surface area59960 Å2
手法PISA
2
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)159,7895
ポリマ－158,4772
非ポリマー1,3123
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-17 kcal/mol
Surface area59710 Å2
手法PISA
単位格子
Length a, b, c (Å)236.940, 158.480, 121.600
Angle α, β, γ (deg.)90.000, 112.830, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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 102 or resid 104...
d_2ens_1(chain "C" and (resid 2 through 102 or resid 104...
d_1ens_2(chain "B" and (resid 326 through 329 or resid 331...
d_2ens_2(chain "D" and (resid 326 through 329 or resid 331...

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_1PROPROILEILEAA2 - 1026 - 106
d_12ens_1PROPROARGARGAA104 - 309108 - 313
d_13ens_1THRTHRASPASPAA322 - 350326 - 354
d_14ens_1ILEILEASNASNAA354 - 497358 - 501
d_15ens_1ARGARGARGARGAA524528
d_16ens_1ASNASNPROPROAA526 - 609530 - 613
d_17ens_1VALVALGLNGLNAA611 - 728615 - 732
d_18ens_1VALVALMETMETAA730 - 739734 - 743
d_19ens_1ARGARGASPASPAA741 - 883745 - 887
d_110ens_1ASNASNGLYGLYAA885 - 887889 - 891
d_111ens_1ILEILELYSLYSAA889 - 941893 - 945
d_112ens_1GLUGLUGLUGLUAA950954
d_113ens_1VALVALTHRTHRAA952 - 974956 - 978
d_114ens_1GLUGLULYSLYSAA976 - 1054980 - 1058
d_115ens_1ASPASPGLNGLNAA1056 - 10641060 - 1068
d_116ens_1R07R07R07R07AE1101
d_21ens_1PROPROILEILECC2 - 1026 - 106
d_22ens_1PROPROARGARGCC104 - 309108 - 313
d_23ens_1THRTHRASPASPCC322 - 350326 - 354
d_24ens_1ILEILEASNASNCC354 - 497358 - 501
d_25ens_1ARGARGARGARGCC524528
d_26ens_1ASNASNPROPROCC526 - 609530 - 613
d_27ens_1VALVALGLNGLNCC611 - 728615 - 732
d_28ens_1VALVALMETMETCC730 - 739734 - 743
d_29ens_1ARGARGASPASPCC741 - 883745 - 887
d_210ens_1ASNASNGLYGLYCC885 - 887889 - 891
d_211ens_1ILEILELYSLYSCC889 - 941893 - 945
d_212ens_1GLUGLUGLUGLUCC950954
d_213ens_1VALVALTHRTHRCC952 - 974956 - 978
d_214ens_1GLUGLULYSLYSCC976 - 1054980 - 1058
d_215ens_1ASPASPGLNGLNCC1056 - 10641060 - 1068
d_216ens_1R07R07R07R07CF1101
d_11ens_2METMETGLNGLNBB326 - 3295 - 8
d_12ens_2ALAALAALAALABB33110
d_13ens_2TRPTRPGLNGLNBB333 - 43312 - 112
d_14ens_2VALVALLEULEUBB445 - 449124 - 128
d_15ens_2GLUGLUSERSERBB451 - 505130 - 184
d_16ens_2GLUGLUILEILEBB507 - 509186 - 188
d_17ens_2LYSLYSARGARGBB511 - 514190 - 193
d_18ens_2GLYGLYILEILEBB516 - 571195 - 250
d_19ens_2LEULEUARGARGBB573 - 574252 - 253
d_110ens_2THRTHRTHRTHRBB576255
d_21ens_2METMETGLNGLNDD326 - 3295 - 8
d_22ens_2ALAALAALAALADD33110
d_23ens_2TRPTRPGLNGLNDD333 - 43312 - 112
d_24ens_2VALVALLEULEUDD445 - 449124 - 128
d_25ens_2GLUGLUSERSERDD451 - 505130 - 184
d_26ens_2GLUGLUILEILEDD507 - 509186 - 188
d_27ens_2LYSLYSARGARGDD511 - 514190 - 193
d_28ens_2GLYGLYILEILEDD516 - 571195 - 250
d_29ens_2LEULEUARGARGDD573 - 574252 - 253
d_210ens_2THRTHRTHRTHRDD576255

NCSアンサンブル:
ID
ens_1
ens_2

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要素

#1: タンパク質 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform


分子量: 124810.422 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PIK3CA / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P42336
#2: タンパク質 Phosphatidylinositol 3-kinase regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PtdIns-3-kinase regulatory subunit p85-alpha


分子量: 33666.961 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PIK3R1, GRB1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P27986
#3: 化合物 ChemComp-YO4 / 2-({(1R)-1-[2-(4,4-dimethylpiperidin-1-yl)-3,6-dimethyl-4-oxo-4H-1-benzopyran-8-yl]ethyl}amino)benzoic acid


分子量: 448.554 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C27H32N2O4 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物 ChemComp-YOR / N-{(3S)-3-(2-methylphenyl)-6-[(oxetan-3-yl)amino]-1-oxo-2,3-dihydro-1H-isoindol-4-yl}-1-benzothiophene-3-carboxamide


分子量: 469.555 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C27H23N3O3S / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物 ChemComp-YNZ / (2S)-N~1~-[(4P)-2-tert-butyl-4'-methyl[4,5'-bi-1,3-thiazol]-2'-yl]pyrrolidine-1,2-dicarboxamide


分子量: 393.527 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C17H23N5O2S2 / タイプ: SUBJECT OF INVESTIGATION
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: 3.56 Å3/Da / 溶媒含有率: 65.47 %
結晶化温度: 289 K / 手法: 蒸気拡散法 / 詳細: 0.4M Sodium Formate, 0.1 M Sodium Citrate, pH 5.2

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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: SSRF / ビームライン: BL19U1 / 波長: 0.97853 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2022年9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: 0.97853 Å / 相対比: 1
反射解像度: 3.35→43.471 Å / Num. obs: 59463 / % possible obs: 99.86 % / 冗長度: 6.2 % / Biso Wilson estimate: 89.42 Å2 / Rpim(I) all: 0.095 / Net I/σ(I): 6.5
反射 シェル解像度: 3.35→3.37 Å / Num. unique obs: 59512 / Rpim(I) all: 0.36

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解析

ソフトウェア名称: PHENIX / バージョン: 1.20.1_4487 / 分類: 精密化
精密化構造決定の手法: 分子置換 / 解像度: 3.35→43.47 Å / SU ML: 0.4725 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.983
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2513 2937 4.94 %RANDOM
Rwork0.2091 56526 --
obs0.2112 59463 99.86 %-
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: 116.69 Å2
精密化ステップサイクル: LAST / 解像度: 3.35→43.47 Å
タンパク質核酸リガンド溶媒全体
原子数20712 0 186 0 20898
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002421358
X-RAY DIFFRACTIONf_angle_d0.616828826
X-RAY DIFFRACTIONf_chiral_restr0.0423093
X-RAY DIFFRACTIONf_plane_restr0.00353680
X-RAY DIFFRACTIONf_dihedral_angle_d14.2248163
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.82409044106
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.36642378282
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.40.40441420.33842707X-RAY DIFFRACTION99.96
3.4-3.460.35981320.30172695X-RAY DIFFRACTION99.96
3.46-3.530.38421540.27852656X-RAY DIFFRACTION99.96
3.53-3.590.29431470.25092667X-RAY DIFFRACTION100
3.59-3.670.28381220.23352713X-RAY DIFFRACTION99.96
3.67-3.750.28041530.22162656X-RAY DIFFRACTION99.96
3.75-3.830.26711310.22232704X-RAY DIFFRACTION99.89
3.83-3.930.29831400.2222684X-RAY DIFFRACTION100
3.93-4.040.25921380.21822654X-RAY DIFFRACTION100
4.04-4.160.25321310.22132705X-RAY DIFFRACTION100
4.16-4.290.24521480.19522681X-RAY DIFFRACTION99.96
4.29-4.440.19571410.1862698X-RAY DIFFRACTION100
4.44-4.620.22221480.18232660X-RAY DIFFRACTION99.93
4.62-4.830.2181350.18492718X-RAY DIFFRACTION99.96
4.83-5.080.2271420.18622689X-RAY DIFFRACTION100
5.08-5.40.23911370.19392688X-RAY DIFFRACTION100
5.4-5.820.26391300.21672715X-RAY DIFFRACTION99.96
5.82-6.40.3011470.23472696X-RAY DIFFRACTION100
6.4-7.330.2141320.22772717X-RAY DIFFRACTION100
7.33-9.210.23881460.18822715X-RAY DIFFRACTION99.93
9.21-43.470.21581410.17512708X-RAY DIFFRACTION97.74
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)
11.64658301956-1.089758117830.09511486596082.55266348576-0.8872235223781.581204405650.08254549254790.0158587697934-0.0382976296769-0.165661458787-0.03515290230150.1614668538140.02741774609870.0740675382506-0.02513370143170.685452796887-0.0462375568562-0.003601185662240.589116579956-0.02656076516460.65666201885133.041137949830.144044992913.4589764535
20.623171938034-0.2773283293810.02189066795421.93196741614-0.8806845891733.86618759578-0.0378797510673-0.189143627491-0.07297901498440.124367385993-0.02462086452550.1863738583630.07238670466090.119859476291-0.05246236344880.532803911926-0.08078710390850.03842893027610.619112150457-0.01563279748310.60977258739335.2179936506-5.1171715537239.6678258092
31.0698803013-0.195379269821-0.07287482146051.958763171530.2159005835262.480897752750.1114395264190.295756338916-0.337233460633-0.747539424043-0.01791890588440.5007617578680.101565434589-0.29122095219-0.0637215537641.039889978230.0064510581981-0.3056223262690.754894779938-0.1621560704860.87857711462726.5711486405-16.4888608945-2.7974894984
41.56894555489-0.220141431811-0.09032730794791.595456017750.02542958622111.235928285470.0607385814898-0.0864567516521-0.146648053326-0.129550467441-0.0667084453339-0.1684816561020.2017269187380.2459254299690.02523915853080.5974248297410.03231054278870.01682696980.575433414218-0.003622291843260.4625063752755.2889714345-6.6377179256718.6620142796
51.639535250820.4621022886492.472606244910.1448102763590.7395789469293.75942794362-0.5789133931350.731707433788-0.13050784624-0.00443813432347-0.04129456971020.543947875434-0.531125504719-0.272210898810.1373294669262.666606363010.1927957555220.1590677033372.241966366310.03083329392312.1002059532542.8296215018-38.1324975655-13.1791603574
60.975004784814-1.24693008986-0.6927690000042.435223790990.9107136447710.3058820405240.3390389502070.202393158471-0.198500313712-0.982695733642-0.265095657487-0.0137777419837-0.2427732191650.103642449876-0.0986613895671.262183550490.1313207624630.01828772750430.959293393193-0.08663502287160.91825160800641.479359861315.4303422029-9.02675501227
72.67799289754-0.644274833660.02619993789811.92546100858-0.00234972427722.76202227073-0.04914164547870.138588715246-0.65654102779-0.1755445400870.120955002171-0.4652459987260.3634792531510.4839471779190.07730515901180.5105792573950.1054903025610.04361855321540.684535356097-0.05869844261581.1527252810763.3042774122-34.897657553189.5947927167
81.08971818417-0.0301599096948-0.3866321639861.422286373660.9880971354380.809937387765-0.0601582039176-0.223523185236-0.2265110914380.04645307174960.13827080098-0.749474427807-0.00813310963770.504527649193-0.2289428699230.507877989422-0.0232120933041-0.07268627880440.97672492117-0.07752067357140.9398786254668.1178244228-14.743264977696.0357915236
92.50491146847-0.217176488968-1.509974933642.128232065110.4061897726332.522277722680.0798359236669-0.3378046095750.1646052842030.0627429281518-0.004583322114410.0346493378775-0.428140260554-0.0227534306726-0.1242877340030.7285114694610.02763096651690.00681414477950.682061957207-0.07010152518150.62287417587833.51061680396.70970109493110.1128824
101.953561343520.168998478942-0.2319728444341.35542310912-0.1215085017530.0382668470739-0.524964652818-0.16979716378-0.59555470158-0.3446706839770.0946182340176-0.7753227503840.006416272328720.4612043749780.2404802749260.846799372295-0.1641434812850.1135197549911.0087433045-0.0626109186841.0219423032872.94157503023.1498748787292.6689928254
111.40683743216-0.315738970667-0.4659921714352.29887217493-0.2347930786141.18759576663-0.008992352203840.2155626302540.0161099748919-1.37957958825-0.128714190024-1.2149584928-0.3892527659970.6671408069070.1384965547731.32589681172-0.4997066893010.6079061317011.47001181149-0.212998979531.6562699644884.167546287511.299774753875.0747372187
121.390704683670.3933331119090.147613065482.134479314460.1430424463121.32633660591-0.07965658357960.03524689867650.192430148367-0.1277249817060.122011175569-0.459993221463-0.3863325217630.388806220378-0.04507753038590.577575968321-0.1746584259820.087904083880.729160986475-0.05020617976520.68226427551158.93182620987.8126085502489.1935479401
132.46200167067-0.2252565965590.4669933572772.1673447760.1945085051412.19854452126-0.06082880451240.2392225364110.22659116-0.2288181778830.0146252429142-0.0130748625889-0.73712322748-0.173443823071-0.004822949558450.9172235681730.02631108385340.07709881412610.6506841647420.08609996422860.57551725010433.695440976312.474643788376.007076293
140.8277186608370.496418319510.5158624527021.878722987420.5631676390451.81277896321-0.09288636923870.3579684353640.443497268776-0.477230050280.008216058957480.0170450572905-0.8455214067520.05657488386380.04009963679461.18987052316-0.1477968838760.1644215373020.7501395569710.09604592032020.86641339488745.977166962520.659563337370.6678909547
150.486379915490.1173027045870.05585467097560.127438080537-0.2626228637750.6998563310840.3462385091710.290267480861-0.182959934976-0.691875426083-0.09339047356740.104196364772-1.681029094720.1250541007460.08177498605792.996941101470.3328215526440.3245200166212.46476288260.1533047567782.5379586951671.23755711338.694936702665.5661915613
160.271644171190.317292761522-0.07725329265841.082987920820.3266697419280.517000141932-0.01282663463690.15638673369-0.175058205906-0.80776943374-0.187702176242-0.5711179435140.01876233394730.4144198403790.2542596173730.912140790554-0.04082621468750.2372717492221.37943291676-0.1727497432721.2391525064172.8974640104-13.965880948568.6824356237
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 2 through 121 )AA2 - 1211 - 120
22chain 'A' and (resid 122 through 296 )AA122 - 296121 - 295
33chain 'A' and (resid 297 through 647 )AA297 - 647296 - 603
44chain 'A' and (resid 648 through 1064 )AA648 - 1064604 - 1017
55chain 'B' and (resid 326 through 428 )BC326 - 4281 - 89
66chain 'B' and (resid 429 through 587 )BC429 - 58790 - 239
77chain 'C' and (resid 2 through 73 )CD2 - 731 - 72
88chain 'C' and (resid 74 through 154 )CD74 - 15473 - 153
99chain 'C' and (resid 155 through 282 )CD155 - 282154 - 281
1010chain 'C' and (resid 283 through 354 )CD283 - 354282 - 340
1111chain 'C' and (resid 355 through 477 )CD355 - 477341 - 458
1212chain 'C' and (resid 478 through 807 )CD478 - 807459 - 763
1313chain 'C' and (resid 808 through 993 )CD808 - 993764 - 942
1414chain 'C' and (resid 994 through 1064 )CD994 - 1064943 - 1013
1515chain 'D' and (resid 326 through 428 )DF326 - 4281 - 89
1616chain 'D' and (resid 429 through 587 )DF429 - 58790 - 239

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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