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- PDB-9azk: Macrocyclic inhibitors targeting the prime site of the fibrinolyt... -

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基本情報

登録情報
データベース: PDB / ID: 9azk
タイトルMacrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin
要素Plasminogen
キーワードHYDROLASE/INHIBITOR / protease inhibitor / fibrinolysis / HYDROLASE-INHIBITOR complex
機能・相同性
機能・相同性情報


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / myoblast differentiation / labyrinthine layer blood vessel development / biological process involved in interaction with symbiont / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of fibrinolysis / negative regulation of cell-substrate adhesion / positive regulation of blood vessel endothelial cell migration / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / protein processing / kinase binding / Schaffer collateral - CA1 synapse / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / : / protease binding / endopeptidase activity / blood microparticle / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
類似検索 - 分子機能
Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
類似検索 - ドメイン・相同性
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: 2.1 Å
データ登録者Guojie, W.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Chemmedchem / 年: 2024
タイトル: Macrocyclic Inhibitors Targeting the Prime Site of the Fibrinolytic Serine Protease Plasmin.
著者: Wiedemeyer, S.J.A. / Wu, G. / Lang-Henkel, H. / Whisstock, J.C. / Law, R.H.P. / Steinmetzer, T.
履歴
登録2024年3月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年10月30日Provider: repository / タイプ: Initial release
改定 1.12025年5月21日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: Plasminogen
B: Plasminogen
C: Plasminogen
D: Plasminogen
E: Plasminogen
F: Plasminogen
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)168,01312
ポリマ－164,0126
非ポリマー4,0016
水10,971609
1
A: Plasminogen
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,0022
ポリマ－27,3351
非ポリマー6671
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Plasminogen
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,0022
ポリマ－27,3351
非ポリマー6671
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Plasminogen
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,0022
ポリマ－27,3351
非ポリマー6671
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Plasminogen
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,0022
ポリマ－27,3351
非ポリマー6671
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Plasminogen
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,0022
ポリマ－27,3351
非ポリマー6671
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Plasminogen
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,0022
ポリマ－27,3351
非ポリマー6671
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)74.851, 128.875, 79.081
Angle α, β, γ (deg.)90.000, 108.064, 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
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 546 through 558 or resid 562...
d_2ens_1(chain "B" and (resid 546 through 558 or resid 562...
d_3ens_1(chain "C" and (resid 546 through 578 or resid 580...
d_4ens_1(chain "D" and (resid 546 through 558 or resid 562...
d_5ens_1(chain "E" and (resid 546 through 558 or resid 562...
d_6ens_1(chain "F" and (resid 546 through 558 or resid 562...

NCSドメイン領域:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PHEPHECYSCYSAA546 - 5585 - 17
d_12VALVALSERSERAA562 - 57821 - 37
d_13ARGARGILEILEAA580 - 59339 - 52
d_14PROPROGLUGLUAA595 - 62354 - 82
d_15HISHISVALVALAA629 - 63588 - 94
d_16ARGARGLEULEUAA637 - 65296 - 111
d_17SERSERPHEPHEAA654 - 681113 - 140
d_18THRTHRTYRTYRAA683 - 713142 - 172
d_19PHEPHETYRTYRAA715 - 753174 - 212
d_110LEULEUPROPROAA755 - 768214 - 227
d_111LYSLYSVALVALAA770 - 777229 - 236
d_112TRPTRPVALVALAA783 - 787242 - 246
d_113ARGARGASNASNAA789 - 791248 - 250
d_114A1AHRA1AHRA1AHRA1AHRAG801
d_21PHEPHECYSCYSBB546 - 5585 - 17
d_22VALVALSERSERBB562 - 57821 - 37
d_23ARGARGILEILEBB580 - 59339 - 52
d_24PROPROGLUGLUBB595 - 62354 - 82
d_25HISHISVALVALBB629 - 63588 - 94
d_26ARGARGLEULEUBB637 - 65296 - 111
d_27SERSERPHEPHEBB654 - 681113 - 140
d_28THRTHRTYRTYRBB683 - 713142 - 172
d_29PHEPHETYRTYRBB715 - 753174 - 212
d_210LEULEUPROPROBB755 - 768214 - 227
d_211LYSLYSVALVALBB770 - 777229 - 236
d_212TRPTRPVALVALBB783 - 787242 - 246
d_213ARGARGASNASNBB789 - 791248 - 250
d_214A1AHRA1AHRA1AHRA1AHRBH801
d_31PHEPHESERSERCC546 - 5725 - 31
d_32ARGARGILEILECC580 - 59339 - 52
d_33PROPROGLUGLUCC595 - 62354 - 82
d_34HISHISVALVALCC629 - 63588 - 94
d_35ARGARGLEULEUCC637 - 65296 - 111
d_36SERSERPHEPHECC654 - 681113 - 140
d_37THRTHRTYRTYRCC683 - 713142 - 172
d_38PHEPHETYRTYRCC715 - 753174 - 212
d_39LEULEUPROPROCC755 - 768214 - 227
d_310LYSLYSVALVALCC770 - 775229 - 234
d_311TRPTRPVALVALCC783 - 781242 - 240
d_312ARGARGASNASNCC789 - 791248 - 250
d_313A1AHRA1AHRA1AHRA1AHRCI801
d_41PHEPHECYSCYSDD546 - 5585 - 17
d_42VALVALSERSERDD562 - 57221 - 31
d_43ARGARGILEILEDD580 - 59339 - 52
d_44PROPROGLUGLUDD595 - 62354 - 82
d_45HISHISVALVALDD629 - 63588 - 94
d_46ARGARGLEULEUDD637 - 65296 - 111
d_47SERSERPHEPHEDD654 - 681113 - 140
d_48THRTHRTYRTYRDD683 - 713142 - 172
d_49PHEPHETYRTYRDD715 - 753174 - 212
d_410LEULEUPROPRODD755 - 768214 - 227
d_411LYSLYSVALVALDD770 - 775229 - 234
d_412TRPTRPVALVALDD783 - 781242 - 240
d_413ARGARGASNASNDD789 - 791248 - 250
d_414A1AHRA1AHRA1AHRA1AHRDJ801
d_51PHEPHECYSCYSEE546 - 5585 - 17
d_52VALVALSERSEREE562 - 57821 - 37
d_53ARGARGILEILEEE580 - 59339 - 52
d_54PROPROGLUGLUEE595 - 62354 - 82
d_55HISHISVALVALEE629 - 63088 - 89
d_56ARGARGLEULEUEE637 - 65296 - 111
d_57SERSERPHEPHEEE654 - 681113 - 140
d_58THRTHRTYRTYREE678 - 713137 - 172
d_59PHEPHETYRTYREE715 - 753174 - 212
d_510LEULEUPROPROEE755 - 768214 - 227
d_511LYSLYSVALVALEE770 - 781229 - 240
d_512TRPTRPVALVALEE783 - 787242 - 246
d_513ARGARGASNASNEE789 - 791248 - 250
d_514A1AHRA1AHRA1AHRA1AHREK801
d_61PHEPHECYSCYSFF546 - 5585 - 17
d_62VALVALSERSERFF562 - 57221 - 31
d_63ARGARGILEILEFF580 - 59339 - 52
d_64PROPROVALVALFF595 - 63554 - 94
d_65ARGARGLEULEUFF637 - 65296 - 111
d_66SERSERPHEPHEFF654 - 681113 - 140
d_67THRTHRTYRTYRFF683 - 713142 - 172
d_68PHEPHETYRTYRFF715 - 753174 - 212
d_69LEULEUPROPROFF755 - 768214 - 227
d_610LYSLYSVALVALFF770 - 781229 - 240
d_611TRPTRPVALVALFF783 - 787242 - 246
d_612ARGARGASNASNFF789 - 791248 - 250
d_613A1AHRA1AHRA1AHRA1AHRFL801

NCS oper:
IDCodeMatrixベクター
1given(-0.99982811106, 0.0141649591184, -0.011962535984), (0.000332578225738, 0.658811271822, 0.752308179878), (0.0185374681583, 0.752174887944, -0.658702740408)11.4066665731, -16.4197216001, 35.5944506114
2given(-0.998669371881, -0.0149662676503, 0.0493507497305), (-0.0218904385267, -0.743445648614, -0.668438012278), (0.0466936223423, -0.668628879417, 0.742128780767)34.7680208066, -31.3080756866, -41.1590847685
3given(0.999001031434, 0.0125533653791, -0.0428876696873), (0.00823592896814, -0.995013400106, -0.0994007197341), (-0.0439216195919, 0.0989482017385, -0.994122801622)-49.2881238988, -43.7695850436, -3.38472968884
4given(-0.999929025272, 0.0115310130916, 0.00299669089467), (-0.00975571223365, -0.936840766942, 0.349620084483), (0.00683889596733, 0.349566035439, 0.936886768169)24.9585114434, -7.39756512225, -29.7911197806
5given(0.99955588911, -0.0270429034325, 0.012518223521), (0.00198153320814, -0.358831945232, -0.933400079605), (0.0297337867135, 0.933010351741, -0.358618997646)13.2768814819, 20.304479972, -2.24029732558

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要素

#1: タンパク質
Plasminogen


分子量: 27335.402 Da / 分子数: 6 / 断片: serine protease domain (UNP residues 561-810) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PLG / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P00747, plasmin
#2: 化合物
ChemComp-A1AHR / (1r,4S)-4-(aminomethyl)-N-[(24S)-5-methyl-8,11,16,23-tetraoxo-7,10,15,22-tetraazatetracyclo[24.2.2.2~18,21~.1~2,6~]tritriaconta-1(28),2(33),3,5,18,20,26,29,31-nonaen-24-yl]cyclohexane-1-carboxamide


分子量: 666.809 Da / 分子数: 6 / 由来タイプ: 天然 / 式: C38H46N6O5 / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 609 / 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
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: 2.26 Å3/Da / 溶媒含有率: 45.54 %
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 / pH: 8.5 / 詳細: 0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2022年4月6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: 0.9537 Å / 相対比: 1
反射解像度: 2.1→47.76 Å / Num. obs: 82977 / % possible obs: 99.75 % / 冗長度: 6.5 % / Biso Wilson estimate: 28.53 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.093 / Rrim(I) all: 0.24 / Net I/σ(I): 7.4
反射 シェル解像度: 2.1→2.21 Å / Rmerge(I) obs: 1.599 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8220 / CC1/2: 0.429 / Rpim(I) all: 0.682 / Rrim(I) all: 1.742 / % possible all: 99.77

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSデータ削減
XDS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
開始モデル: PDB entry 5UGD

5ugd


解像度: 2.1→47.76 Å / SU ML: 0.2833 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 27.4763
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2549 4059 4.9 %
Rwork0.237 78718 -
obs0.2379 82777 99.76 %
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: 40.26 Å2
精密化ステップサイクル: LAST / 解像度: 2.1→47.76 Å
タンパク質核酸リガンド溶媒全体
原子数11223 0 294 609 12126
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.012812008
X-RAY DIFFRACTIONf_angle_d1.649916388
X-RAY DIFFRACTIONf_chiral_restr0.0951792
X-RAY DIFFRACTIONf_plane_restr0.00372113
X-RAY DIFFRACTIONf_dihedral_angle_d13.2334380
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.875196135977
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.809839620331
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.808360608114
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.874089440956
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.853686712867
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.33271340.32742706X-RAY DIFFRACTION99.72
2.12-2.150.30731400.31462699X-RAY DIFFRACTION99.79
2.15-2.180.36611380.31122658X-RAY DIFFRACTION99.79
2.18-2.210.31791290.31212756X-RAY DIFFRACTION99.38
2.21-2.240.4131180.35162660X-RAY DIFFRACTION98.93
2.24-2.270.4421320.42072690X-RAY DIFFRACTION96.68
2.27-2.30.27791390.29822630X-RAY DIFFRACTION99.96
2.3-2.340.29551410.27822747X-RAY DIFFRACTION100
2.34-2.380.29291620.28022706X-RAY DIFFRACTION100
2.38-2.420.27911440.29032697X-RAY DIFFRACTION100
2.42-2.460.31131280.28682731X-RAY DIFFRACTION100
2.46-2.510.30631440.28522696X-RAY DIFFRACTION100
2.51-2.560.30161520.28472721X-RAY DIFFRACTION100
2.56-2.620.32981600.27462683X-RAY DIFFRACTION100
2.62-2.680.28291320.27542731X-RAY DIFFRACTION99.62
2.68-2.740.2891490.27542720X-RAY DIFFRACTION100
2.74-2.820.31231390.25542705X-RAY DIFFRACTION99.93
2.82-2.90.29821340.25412730X-RAY DIFFRACTION100
2.9-2.990.2371470.25742713X-RAY DIFFRACTION100
2.99-3.10.28271370.25172718X-RAY DIFFRACTION99.96
3.1-3.230.28481600.24052696X-RAY DIFFRACTION100
3.23-3.370.2491490.22192720X-RAY DIFFRACTION99.97
3.37-3.550.19861630.20482704X-RAY DIFFRACTION100
3.55-3.770.20721110.21162752X-RAY DIFFRACTION99.48
3.77-4.060.18711200.17842728X-RAY DIFFRACTION100
4.06-4.470.19541300.1672745X-RAY DIFFRACTION100
4.47-5.120.18151530.16452734X-RAY DIFFRACTION100
5.12-6.450.23041230.20742758X-RAY DIFFRACTION100
6.45-47.760.23011510.22252784X-RAY DIFFRACTION99.83
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.48732058837-1.03299231843-0.3823991249522.988283086263.29669703523.95843216-0.3511991629980.72949368649-0.360493088082-0.3645920417960.137053679196-0.5812312099680.229306560266-0.1840005391790.2248188482830.11412003070.023338785098-0.01287926130640.158801826141-0.002707488731340.14751322421735.8523979276-13.063005820714.4414011872
22.590542890110.3097231690880.5754428285941.92137091706-0.04153303118851.698674867990.00678995334414-0.135023848557-0.0146716889790.0933880414818-0.06012746723490.08511042958460.0666849072908-0.07145545155290.04894756276380.152804858474-0.00921601767814-0.01647518478730.140759947621-0.01279580501030.072705501072921.172185743-11.47717201616.8488227592
36.953669326512.07328779944-2.250098006655.75027111734-2.398100215041.99881095612-0.0911662319279-0.232127948787-0.5667634108680.063501530739-0.1144595291880.1721090375750.38693928003-0.04545189856650.09275816977350.172467862188-0.006961676989180.006850194621130.122192432488-0.05275979278550.242025001541-24.6316163507-14.220993248316.9774502895
43.522820856950.7600238997420.6913876866281.895506313380.1285273692142.639832036250.0287370167844-0.02358560411160.1693790933150.07536325097650.0528599020101-0.226027921273-0.2500408659320.13954627649-0.1017688116590.1576221869650.02116284934980.006223044284280.176254961807-0.0276159415310.199227390237-16.9868519217-3.1718254058518.1307606502
52.10039100318-0.4675096425040.80719901991.71895288924-0.4182835273291.265614946520.0173763776656-0.400343214720.3747966052220.1727474945650.038794991212-0.116713573709-0.2181127059050.169439448476-0.07196208211830.207045030885-0.0139571076534-0.003967107316520.250138860319-0.1033230832470.202828505529-6.61818501816-4.26951165323.677698763
63.00355831346-0.2168774720790.1284726565851.8590818835-0.1886038042650.7741511706320.0214376928994-0.2308074711070.202793004490.0973352937133-0.0206084582275-0.0482174154835-0.0702625463573-0.0494904142945-0.007032907729530.164461375773-0.0288696499909-0.002786492054030.209593415475-0.01744495050870.11607174418-12.598095871-10.348534363621.8725681248
74.66953134541-1.71429466639-2.479716276746.464924349142.404312024256.846400574450.64469789580.9329987568961.32500555512-0.6863507682250.196827254580.1159443291-1.00771426223-0.0406101992458-0.4924700130810.239338771299-0.0162173311831-0.02209494396180.3203951158920.06089294183170.321404626387-16.9435697579-1.070454698036.25402062278
83.25550318946-0.5528725519320.1247568776462.67639985644-0.6956979494113.212197130940.07544551223560.508749636845-0.160288827935-0.421954023594-0.0997144618542-0.1487588554850.4314297262660.293265278210.01228782324810.2410921112690.01342443242540.00156732960980.23549727708-0.03187186624510.157258623868-6.04586122251-17.07811592333.9041633787
92.9848226482-0.0299577242372-0.1094624057981.64418429698-0.8019852908233.386958660550.0252256422181-0.162215119993-0.0557226505574-0.104783304877-0.04024869536550.01343607788420.2219251944250.07052888841360.05246280573770.1240436020950.00187686246327-0.00530374005170.113456394154-0.03399079229730.146140808391-8.41045878017-17.713017539215.8472947152
104.87016149223-1.937494643290.7278598682314.98122525724-1.745571606572.979628596510.0548616235240.194065043261-0.0950094159171-0.222228569533-0.2214544044050.648471020051-0.0658860703342-0.4968275300680.1900388036080.200212439802-0.08141286233680.01797203314220.304566597228-0.1478892211210.4239603477214.41376690593-38.2040044004-20.1014839205
111.831553612920.1440140229880.2608365016172.619018440710.3416117754491.65514524748-0.04940062343940.33496917564-0.391730820279-0.0674489831992-0.06216825198020.2964317638580.079596799209-0.1542899272770.1033779870620.207008774378-0.0141251645007-0.003928473283560.305042921583-0.1867075254620.35442141956413.9596789925-38.2483525981-25.7324004465
123.726452022510.7861231912350.3622674634272.262465569931.357287833962.70158899791-0.0396539552956-0.368379864528-0.2404651200570.211838847352-0.1566346173530.0825599925629-0.0254450738383-0.09991592238940.1585602731520.1965472160040.01502283993230.0177960222580.206167003729-0.05796380919650.22341442073417.073260486-30.6815656913-8.63606624306
132.22634776220.3163661399480.7953355276542.284058683750.1421884833.49603430383-0.0769955520450.288778877377-0.174104571557-0.1080400435960.05398922708930.31484450671-0.1671112680440.07556786565180.06779541314120.172511065007-0.050719667522-0.007006985046120.207547964147-0.1323344717570.22496489632516.2246887283-28.0965096614-20.7423957967
144.63126198932-1.509969686790.1592595486531.42292177152-0.5836940848756.959376859060.00222876765145-0.195631022685-0.3880884317580.0548328629-0.284815541026-0.7915967101710.1512371778260.5679832837580.1963800375460.2462990687160.0219385993341-0.02549475245570.2891135544110.1573814466020.538486703083-21.27605215-37.7194104103-22.9756454847
153.590323362870.229598078379-1.003647951862.16794228475-0.08307177730182.287958069750.0532795773945-0.0522550708606-0.298518358288-0.0602696574667-0.113159116776-0.5832244405490.09709432583930.08581023523990.01735606844130.258328661202-0.00762232131219-0.04067393182070.2728906454580.1223514488240.425952108912-27.8305668619-36.9860421793-22.4713803385
163.729876197010.188508806433-1.202519841733.360543294830.595909314963.477837551170.302826858247-0.1170898469860.340219371148-0.0956580553737-0.153145969781-0.597416813065-0.292021723804-0.186429061068-0.07653387913890.2249897843490.03182624608630.002927850312610.2699789517390.09933624826760.355715338003-32.6459533207-26.4109405868-21.48037759
176.726414820592.27184377599-0.5319609618457.516159554152.526329142945.00292406774-0.1545749707750.2187309306830.1481477344030.08029605605520.1104577552081.03943471896-0.230487592330.0136673629291-0.02353720634740.2708175147040.04004029733950.07022963533040.2769871714340.07341137409830.306334946171-6.904473665087.46536252137-15.3488125669
181.989891102160.698291746061-0.6933791532084.11694805249-0.490902466911.458223163650.0601055108324-0.0178461386550.149394381130.0265557680870.04635135182910.144536658969-0.0272079329058-0.0184032464701-0.1129947949780.2680384166430.030154679694-0.008822203104790.2859588250910.01341206964410.2311135299814.079478981448.86998945907-16.7942236446
193.13367967092-0.800230489973-1.235381113895.424150888381.345783666382.741843939910.1017330881770.3555746928430.234359990251-0.1993269551110.05687982232940.04664842326580.0934771756238-0.0634117568697-0.1463229320450.2921040012790.003787932346850.02336330621120.2527635974860.07532682594720.1835970422935.5268932533911.2933017876-23.8519535708
208.032820413820.2961254532241.252313530966.676276802263.845349081712.641013133690.222082243546-0.323888943922-0.239813890655-0.166845256093-0.00704255842423-0.30356984538-0.109582126580.847049960227-0.1742900167220.44247353910.080408658966-0.0239918644630.7124771792340.2052649923170.46223117173243.78877182926.11229664712-16.3102527945
217.1287296280.343826612816-1.017205549474.709056189820.07846710222911.61097916975-0.0346696191099-0.550147159198-0.1739348909550.207086126326-0.13409635694-0.544778954695-0.2323910634330.2998584447820.1092270070440.437074164005-0.0349223386864-0.01555789881160.6909616362390.144759344720.46698883321533.04384709413.823182692-7.21465659308
226.89346020959-0.8444690552060.7657222754632.51816586146-0.4923302015563.849883134270.1078879497640.2319550276840.288751278184-0.237183423475-0.320052097481-0.2294693027720.1716461115080.4021593348470.2043868608570.3683421389930.01864796651580.02860571110220.4899182183870.08824689419040.45662038033134.050791464211.6702665971-22.6769782352
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 544 through 565 )AA544 - 5651 - 20
22chain 'A' and (resid 566 through 791 )AA566 - 79121 - 246
33chain 'B' and (resid 544 through 565 )BC544 - 5651 - 20
44chain 'B' and (resid 566 through 585 )BC566 - 58521 - 40
55chain 'B' and (resid 586 through 618 )BC586 - 61841 - 73
66chain 'B' and (resid 619 through 684 )BC619 - 68474 - 139
77chain 'B' and (resid 685 through 697 )BC685 - 697140 - 152
88chain 'B' and (resid 698 through 743 )BC698 - 743153 - 198
99chain 'B' and (resid 744 through 791 )BC744 - 791199 - 246
1010chain 'C' and (resid 545 through 585 )CE545 - 5851 - 38
1111chain 'C' and (resid 586 through 684 )CE586 - 68439 - 137
1212chain 'C' and (resid 685 through 743 )CE685 - 743138 - 196
1313chain 'C' and (resid 744 through 791 )CE744 - 791197 - 244
1414chain 'D' and (resid 546 through 600 )DG546 - 6001 - 53
1515chain 'D' and (resid 601 through 710 )DG601 - 71054 - 163
1616chain 'D' and (resid 711 through 791 )DG711 - 791164 - 244
1717chain 'E' and (resid 545 through 585 )EI545 - 5851 - 39
1818chain 'E' and (resid 586 through 743 )EI586 - 74340 - 197
1919chain 'E' and (resid 744 through 791 )EI744 - 791198 - 245
2020chain 'F' and (resid 546 through 594 )FK546 - 5941 - 47
2121chain 'F' and (resid 595 through 640 )FK595 - 64048 - 88
2222chain 'F' and (resid 641 through 791 )FK641 - 79189 - 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