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- PDB-3sud: Crystal structure of NS3/4A protease in complex with MK-5172 -

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基本情報

登録情報
データベース: PDB / ID: 3sud
タイトルCrystal structure of NS3/4A protease in complex with MK-5172
要素NS3 protease, NS4A protein
キーワードHYDROLASE/INHIBITOR / drug resistance / drug design / Protease inhibitors / HCV / serine protease / VIRAL PROTEIN / HYDROLASE-INHIBITOR complex
機能・相同性
機能・相同性情報


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
類似検索 - 分子機能
Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily ...Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Trypsin-like serine proteases / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
類似検索 - ドメイン・相同性
Chem-SUE / Genome polyprotein
類似検索 - 構成要素
生物種Hepatitis C virus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.96 Å
データ登録者Schiffer, C.A. / Romano, K.P.
引用ジャーナル: Plos Pathog. / 年: 2012
タイトル: The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors.
著者: Romano, K.P. / Ali, A. / Aydin, C. / Soumana, D. / Ozen, A. / Deveau, L.M. / Silver, C. / Cao, H. / Newton, A. / Petropoulos, C.J. / Huang, W. / Schiffer, C.A.
履歴
登録2011年7月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年9月19日Provider: repository / タイプ: Initial release
改定 1.12017年8月23日Group: Refinement description / Source and taxonomy / カテゴリ: entity_src_gen / software
改定 1.22017年11月8日Group: Refinement description / カテゴリ: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
改定 1.32019年12月11日Group: Advisory / Database references / Structure summary
カテゴリ: chem_comp / pdbx_distant_solvent_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details
改定 1.42024年2月28日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: NS3 protease, NS4A protein
B: NS3 protease, NS4A protein
C: NS3 protease, NS4A protein
D: NS3 protease, NS4A protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)89,37513
ポリマ－85,9494
非ポリマー3,4259
水3,495194
1
A: NS3 protease, NS4A protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,4164
ポリマ－21,4871
非ポリマー9283
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: NS3 protease, NS4A protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,3203
ポリマ－21,4871
非ポリマー8322
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: NS3 protease, NS4A protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,3203
ポリマ－21,4871
非ポリマー8322
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: NS3 protease, NS4A protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)22,3203
ポリマ－21,4871
非ポリマー8322
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)56.133, 102.698, 73.289
Angle α, β, γ (deg.)90.00, 112.54, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
NS3 protease, NS4A protein


分子量: 21487.330 Da / 分子数: 4
断片: NS4A (UNP residues 1674-1688), NS3 (UNP residues 1027-1208)
変異: A1027S, P1028G, I1029D, L1039E, L1040E, I1043Q, I1044E, L1047Q, A1066T, C1073S, C1078L, I1098T, P1112Q, S1165A, C1185S, C1679S, V1686I
由来タイプ: 組換発現 / 由来: (組換発現) Hepatitis C virus (ウイルス) / 株: subtype 1a, BID-V318 / 遺伝子: NS3-NS4A / プラスミド: PET28a / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A8DG50
#2: 化合物
ChemComp-SUE / (1aR,5S,8S,10R,22aR)-5-tert-butyl-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-14-methoxy-3,6-di oxo-1,1a,3,4,5,6,9,10,18,19,20,21,22,22a-tetradecahydro-8H-7,10-methanocyclopropa[18,19][1,10,3,6]dioxadiazacyclononadec ino[11,12-b]quinoxaline-8-carboxamide / Grazoprevir, MK-5172 / グラゾプレビル


分子量: 766.903 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C38H50N6O9S / コメント: プロテアーゼ阻害剤*YM
#3: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 1 / 由来タイプ: 合成 / 式: SO4
#4: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 194 / 由来タイプ: 天然 / 式: H2O
非ポリマーの詳細MK-5172 IS A MACROCYCLIC, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM MERCK. THE DRUG MIMICS ...MK-5172 IS A MACROCYCLIC, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM MERCK. THE DRUG MIMICS THE PEPTIDE BACKBONE OF PROTEINS, ALTHOUGH THE DRUG MOIETIES CANNOT BE SEQUENCED USING AMINO ACID NOMENCLATURE.
配列の詳細THE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY ...THE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1678-1688 OF DATABASE SEQUENCE REFERENCE (UNP A8DG50). THIS PEPTIDE IS COVALENTLY LINKED TO THE N-TERMINUS OF NS3. C1679S MUTATION WAS ENGINEERED TO PREVENT DISULFIDE FORMATION. THE V1686I AND I1687N WERE ENGINEERED TO OPTIMIZE THE LINKER BETWEEN THE COFACTOR 4A AND NS3.

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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: 2.27 Å3/Da / 溶媒含有率: 45.82 %
結晶化温度: 295 K / 手法: ハンギングドロップ法, 蒸気拡散法 / pH: 6.2
詳細: 20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 21-ID-F / 波長: 0.97872 Å
検出器日付: 2011年3月31日
放射プロトコル: SINGLE WAVELENGTH / 散乱光タイプ: x-ray
放射波長波長: 0.97872 Å / 相対比: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.548
11-H, -K, H+L20.452
反射解像度: 1.96→50 Å / Num. obs: 50198 / % possible obs: 91.6 % / 冗長度: 2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 10
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsDiffraction-ID% possible all
1.96-2.031.90.195192.6
2.03-2.111.90.186191.5
2.11-2.211.90.15191.1
2.21-2.321.90.144190.1
2.32-2.471.90.121189.3
2.47-2.661.90.113189.6
2.66-2.9320.096192
2.93-3.352.10.081194.4
3.35-4.222.30.058194.3
4.22-502.40.041191.4

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
REFMAC精密化
PDB_EXTRACT3.1データ抽出
精密化構造決定の手法: 分子置換 / 解像度: 1.96→36.48 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 7.62 / SU ML: 0.124 / SU R Cruickshank DPI: 0.0391 / 交差検証法: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.036 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.23749 2586 5.2 %RANDOM
Rwork0.184 ---
obs0.18679 47569 91.26 %-
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: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 23.965 Å2
Baniso -1Baniso -2Baniso -3
1-21.6 Å20 Å21.15 Å2
2---0.31 Å20 Å2
3----21.29 Å2
精密化ステップサイクル: LAST / 解像度: 1.96→36.48 Å
タンパク質核酸リガンド溶媒全体
原子数5326 0 225 194 5745
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.010.025685
X-RAY DIFFRACTIONr_bond_other_d0.0080.023606
X-RAY DIFFRACTIONr_angle_refined_deg1.4292.0067824
X-RAY DIFFRACTIONr_angle_other_deg1.3573.0098851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7755762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98322.788165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79215760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2861534
X-RAY DIFFRACTIONr_chiral_restr0.1270.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021099
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4811.53781
X-RAY DIFFRACTIONr_mcbond_other0.1021.51575
X-RAY DIFFRACTIONr_mcangle_it0.8326058
X-RAY DIFFRACTIONr_scbond_it1.27131904
X-RAY DIFFRACTIONr_scangle_it1.9254.51727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 1.96→2.012 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.247 191 -
Rwork0.208 3392 -
obs--88.34 %
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)
11.4333-0.156-0.97773.45730.10570.66760.0258-0.12340.02560.1247-0.0098-0.0007-0.01830.0935-0.0160.0368-0.01960.0670.1530.01020.156722.65159.01278.6241
21.43960.62010.02830.26740.01220.0008-0.04270.20.2705-0.0190.06070.11980-0.0038-0.0180.40210.0056-0.03540.3613-0.02810.187513.09173.3328-8.0179
36.66294.40648.36334.85375.446211.01580.3559-0.22770.03080.1972-0.19720.07910.3027-0.0277-0.15870.1031-0.03280.1090.1962-0.03640.143225.65477.2974-0.1285
42.770.4935-1.94260.339-1.29454.94570.3388-0.0895-0.24230.079-0.14250.0533-0.31360.5637-0.19630.1608-0.0210.02870.1938-0.02210.208628.628815.640710.7462
50.6050.86010.52281.23020.72921.8018-0.04560.00930.0109-0.08640.011-0.02140.1810.09680.03460.07550.00750.08230.1330.00910.185220.7198.04276.0747
60.8869-0.0476-0.33941.5460.14050.48810.06180.10080.0865-0.0612-0.02090.06750.0750.0108-0.04090.0657-0.02070.03540.13740.01050.120412.44716.99918.5068
71.34810.55840.82840.5301-0.24571.68060.0083-0.00510.02270.03310.05160.0276-0.0358-0.1289-0.05990.07240.01310.0270.122400.140914.26364.297615.5054
81.48710.4895-1.1572.3373-1.13751.27160.0653-0.01190.04670.1183-0.0107-0.1214-0.20560.007-0.05460.1421-0.01250.06740.1202-0.02930.11115.808811.827517.8696
90.02830.001-0.04660.0543-0.36532.52880.0648-0.01980.0334-0.0002-0.00190.0061-0.09430.0253-0.0630.1448-0.00660.07720.147-0.01550.166912.78246.953116.6106
100.7591.4607-0.13692.8172-0.20741.19840.03660.01910.08950.06450.01810.1515-0.0383-0.0887-0.05470.03720.02570.04580.14080.0050.17496.613710.9644.6545
114.97950.6344-0.54580.40760.0631.75640.21510.1745-0.1650.0534-0.06030.0286-0.0215-0.0293-0.15490.08380.00250.05290.1072-0.00120.13138.3131-5.30020.8297
120.42290.36250.68062.54941.4421.42840.0378-0.02150.00730.1855-0.11370.18650.1477-0.07130.07590.1358-0.0220.03650.15470.02310.14664.2812-11.77987.1551
1310.32954.40648.573515.57671.76313.2526-0.0995-0.12270.0779-0.84210.05350.1720.1457-0.05610.0460.09540.02050.07980.1392-0.01310.204618.4237-12.92244.8744
142.02550.59312.00111.89050.83122.0140.00250.22890.01850.0706-0.0006-0.08030.00930.2021-0.00190.05450.00510.06230.14590.01520.117114.3406-3.45357.2018
152.37531.13564.52163.0483-1.222213.18970.05620.1422-0.04730.02810.25540.17560.09540.035-0.31160.03460.00930.03180.1371-0.01050.17372.58191.02893.0763
162.47890.33791.07950.04690.14570.47440.0828-0.0737-0.22760.01920.0122-0.0260.0047-0.039-0.0950.17060.0410.09130.15130.00510.140412.2241-12.211911.9252
173.1881.5018-0.76621.6206-2.87837.2223-0.02240.015-0.04950.1075-0.0103-0.0212-0.3538-0.16070.03270.12380.06270.00560.2466-0.05940.1562.8619-0.361712.7358
186.1114.01341.89132.70071.28820.6182-0.31310.19480.3863-0.1070.18390.2809-0.02930.10130.12920.17860.07430.08550.2415-0.01290.19871.39527.130216.6027
190.90740.4221-0.92953.0172-1.21014.0325-0.0947-0.0356-0.00150.1031-0.0775-0.0047-0.1362-0.02670.17210.0579-0.01640.04350.14270.02230.16243.592525.4178-6.8357
202.1289-3.15972.36655.9363-1.17357.02460.19140.23840.0757-0.4609-0.2759-0.1147-0.19540.38050.08450.1559-0.0480.06890.2380.00730.159113.610731.053-24.2581
211.3902-0.2186-3.55780.45310.76659.22840.0045-0.24040.03620.0066-0.0390.21050.06850.53760.03450.1223-0.02520.0630.190.00990.18831.600726.399-17.8319
223.3998-2.19370.69754.5833-0.70835.3357-0.044-0.02580.086-0.03450.0923-0.22350.1669-0.1212-0.04830.036-0.02210.04290.15580.01460.1357-0.99119.5396-8.0697
231.8318-0.5270.25771.4528-1.05220.7765-0.13980.3455-0.0895-0.14070.1102-0.05490.1-0.10810.02960.0981-0.03840.07110.1641-0.01750.142210.83623.5277-16.5532
246.1144-0.8318-0.60170.62130.10150.0617-0.0688-0.0431-0.01360.11120.05740.03740.00690.0160.01130.07480.00220.04120.13340.00430.13428.250931.1402-8.3046
250.19930.2954-0.09140.4696-0.25420.81920.0030.0382-0.00760.03630.04660.02010.06220.0755-0.04960.09890.01420.04290.1270.01680.152414.330129.2816-3.0952
260.44981.17511.13023.39432.30464.17510.02270.0022-0.0040.0717-0.0438-0.0020.04650.04280.0210.04530.00340.05950.1487-0.01640.13868.721419.2556-2.8633
270.3755-0.1731-0.2951.0379-0.62040.8302-0.0502-0.06340.01150.08540.053-0.0331-0.01630.0261-0.00270.04650.0120.02790.1412-0.00590.143216.469827.7937-0.3521
283.13842.8791.19092.82111.19730.52640.0701-0.05520.07480.0351-0.0548-0.02770.0342-0.0025-0.01540.06150.00270.04190.14710.01970.159521.965524.1587-14.425
297.09320.1387-1.14970.83290.79961.0405-0.14810.05220.1967-0.04950.10740.0394-0.07810.02250.04070.17810.04280.02760.1775-0.01520.161424.108339.3443-16.4279
304.59612.7091.32043.24291.77322.5317-0.1331-0.11680.3307-0.0228-0.06530.1697-0.2222-0.11930.19840.1255-0.00340.05120.16650.01910.118819.750643.6156-15.8386
314.6430.1835-0.08823.7599-2.05551.1239-0.07650.03980.3935-0.19790.0438-0.06480.1053-0.02520.03270.08940.00480.0430.1474-0.05790.131617.110148.5894-12.5107
321.237-0.5802-0.74910.28820.26710.98020.07960.04090.1715-0.02190.0052-0.078-0.1849-0.0796-0.08480.085-0.00450.02380.13850.00280.175615.638539.3709-13.7065
330.18050.78020.21493.92510.06561.62140.01470.0243-0.052-0.05890.0911-0.21680.23120.0822-0.10580.05060.00330.0310.1537-0.00830.126623.142634.9702-13.0207
341.3045-1.24330.00622.3579-0.59160.2963-0.0312-0.00160.13670.20470.0489-0.1022-0.0834-0.045-0.01770.09520.01360.03730.159-0.01310.1516.609346.8579-6.4712
352.7883-0.32822.5115.27-2.94193.6064-0.08230.0967-0.09520.00860.0215-0.2809-0.05960.10420.06080.06550.06180.04250.1889-0.00930.161426.683530.2987-2.7131
360.8287-0.59530.01571.6337-1.19491.1625-0.02240.0815-0.0129-0.00340.10850.09740.0193-0.1732-0.0860.0808-0.00590.04760.14510.00440.159525.85626.3486-17.1507
370.00370.0137-0.00526.924-2.20070.6998-0.0174-0.0116-0.02040.9282-0.1512-0.5265-0.29510.05060.16860.2709-0.07650.01210.3532-0.05940.220235.206212.1866-1.9172
3810.28113.2338-0.17472.42840.40940.1578-0.05660.2840.0966-0.150.05210.015-0.03780.00020.00450.07300.08780.20160.02150.128524.96757.1856-7.425
393.4356-0.31030.96671.0748-0.98281.04070.00690.12130.0421-0.04690.16910.23260.0537-0.1333-0.1760.0866-0.01420.070.1788-0.01910.151618.39547.6984-18.767
401.03510.8823-0.36793.12210.62910.59740.0052-0.0355-0.0275-0.03720.0517-0.0197-0.0578-0.0745-0.05690.06710.01610.0680.19720.03540.13329.01465.343-15.7264
411.90420.56031.43780.57140.70981.2922-0.0057-0.0487-0.020.0345-0.001-0.00860.0133-0.0440.00670.07230.01490.04940.1343-0.02280.138435.46248.068-17.4796
420.5822-0.2757-0.30310.81860.01560.2057-0.01360.0812-0.04050.0261-0.01640.1394-0.0303-0.0660.02990.08530.01830.01780.1282-0.01610.156131.26736.8768-24.4955
431.6080.5448-0.76430.2044-0.16630.88430.0010.06870.1069-0.03980.03240.0302-0.1481-0.0572-0.03340.1050.01420.01610.12480.00960.157832.31838.9513-29.9367
445.584-1.9359-0.71844.18981.56920.58780.1370.26480.1834-0.1294-0.0712-0.1765-0.0501-0.0274-0.06580.07440.01630.0620.15270.02450.104940.69063.9334-27.4467
452.03470.85283.759512.48716.2318.7401-0.1116-0.01210.1159-0.3991-0.31410.5379-0.3615-0.17380.42570.17010.07610.1390.1425-0.03040.263729.891315.3958-22.5188
460.02350.1509-0.04061.8489-0.50520.6477-0.0382-0.0309-0.01190.14850.0168-0.2778-0.1452-0.00430.02140.21230.05190.00330.1824-0.03370.167245.964814.9244-12.7158
477.1190.9897-1.14973.5555-1.55350.75790.2448-0.1847-0.1750.092-0.21890.1261-0.04040.0883-0.02590.1504-0.09860.06470.2172-0.03260.090839.44132.8601-6.9845
485.1008-0.77170.02480.92030.49643.69030.00860.0454-0.02590.0181-0.0921-0.039-0.01070.21040.08350.0682-0.01750.05280.11080.02080.133151.92322.6972-9.2866
492.39570.68760.48841.30980.04381.7340.0203-0.12350.05370.16490.0086-0.10.1414-0.0524-0.02890.1108-0.00490.04730.10950.00130.116845.934-5.0848-8.6905
500.02090.11160.15920.9810.83241.91420.0227-0.01650.02150.1502-0.0134-0.04560.002-0.0553-0.00920.0879-0.01570.0520.1494-0.01760.157742.14766.0199-11.182
511.14312.08060.20315.10631.43150.8937-0.01750.0406-0.0556-0.030.0473-0.15540.0034-0.0204-0.02970.0823-0.00230.02940.12680.01350.169344.72940.5441-16.4838
521.09260.7298-0.679.2589-4.77022.54120.01270.04840.0002-0.0435-0.0755-0.12880.01610.02630.06280.1072-0.00020.03820.13930.02410.112947.3261-6.6046-13.2956
532.89086.78023.334923.55463.86625.8924-0.27390.24440.2774-0.7846-0.05930.645-0.23880.6140.33310.192-0.02110.11530.17180.10180.224846.98879.5122-22.1308
541.2375-0.12290.43060.78320.71811.9429-0.0682-0.0634-0.16750.0969-0.1229-0.0299-0.08930.03690.19110.10990.02710.01880.20120.04630.227627.362629.173836.3214
550.9014-0.90380.45963.00091.54362.15320.10680.14420.0147-0.29120.0202-0.1724-0.13930.2296-0.1270.10710.0160.0390.18540.04120.159330.845329.386741.745
562.3092-0.38891.14840.0682-0.19070.5753-0.00350.079-0.07050.02010.01390.02710.00240.068-0.01050.17880.03270.11530.26420.02190.173836.792328.897431.2899
573.01661.01960.02380.8184-1.55975.2522-0.0683-0.03440.1755-0.0273-0.06210.0485-0.01040.27590.13030.0919-0.02940.04560.19440.04030.205428.356635.348531.8375
580.8025-0.4914-0.16140.30760.09240.03880.02110.0531-0.0075-0.0324-0.0503-0.03090.011-0.00090.02920.11620.02350.0760.14160.02750.19921.536929.03231.7114
590.8867-0.7317-0.04942.8944-2.53612.90350.01850.0282-0.0087-0.1583-0.1297-0.09930.14680.10440.11130.10480.01470.04740.1336-0.00680.112120.670529.917325.7287
602.22050.25332.0633.2550.92462.06420.21580.1548-0.10340.064-0.0913-0.14410.21210.1273-0.12450.13520.08190.11360.22470.02530.161731.049227.298521.6306
610.332-0.7888-0.0114.7981-0.15740.0137-0.14980.05220.0451-0.02480.1415-0.13890.0409-0.00880.00830.20160.01840.04520.13390.00780.117918.308730.752120.6296
624.94481.7271-7.84270.6034-2.739912.4414-0.0948-0.4566-0.1276-0.044-0.1461-0.04970.19350.72120.24090.21130.05830.19040.2129-0.01010.242524.480319.123431.2862
631.67070.3449-0.05182.4578-0.94230.7001-0.025-0.06750.0348-0.044-0.00070.20840.0711-0.17560.02570.09060.0060.04510.13940.00690.13248.505926.165438.241
643.3475-1.9324-0.05151.2633-0.56792.4449-0.1315-0.10840.0990.07150.0494-0.0733-0.0298-0.00050.08210.1268-0.00160.02710.1106-0.00020.152411.790234.301940.9745
651.7698-0.5585-1.31773.5411-0.59321.28420.07240.0793-0.13850.1034-0.16110.1292-0.0824-0.02160.08870.0689-0.02770.05620.15040.00980.13656.710638.505539.607
660.1581-0.5755-0.41363.32830.39362.42260.0015-0.0680.00910.01350.0035-0.1148-0.11090.2462-0.0050.0632-0.00230.03520.1703-0.01090.119818.452341.865737.8926
674.3172-0.7371-1.08380.13430.26721.37470.055-0.02680.0928-0.00020.00130.00230.0587-0.0944-0.05620.0898-0.01760.04380.10150.02340.187111.365525.137737.3302
681.2839-0.1734-0.23011.9634-0.39610.14930.02270.071-0.1008-0.0047-0.0380.0979-0.0162-0.04820.01530.09120.01640.03230.1666-0.01690.125610.69741.721334.1388
692.99421.5405-0.442213.39636.06153.2034-0.1092-0.21330.04850.2697-0.08270.41630.18140.04280.19190.1417-0.01260.01820.1280.01040.11859.032728.818828.4425
700.574-1.9395-1.46986.59164.399612.09850.006-0.0165-0.0665-0.07440.0610.24620.6697-0.1499-0.0670.142-0.05330.08770.1141-0.01070.163212.2123.728322.106
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A989 - 998
2X-RAY DIFFRACTION2A999 - 1005
3X-RAY DIFFRACTION3A1006 - 1014
4X-RAY DIFFRACTION4A1015 - 1026
5X-RAY DIFFRACTION5A1027 - 1041
6X-RAY DIFFRACTION6A1042 - 1051
7X-RAY DIFFRACTION7A1052 - 1058
8X-RAY DIFFRACTION8A1059 - 1080
9X-RAY DIFFRACTION9A1081 - 1085
10X-RAY DIFFRACTION10A1086 - 1098
11X-RAY DIFFRACTION11A1099 - 1115
12X-RAY DIFFRACTION12A1116 - 1129
13X-RAY DIFFRACTION13A1130 - 1134
14X-RAY DIFFRACTION14A1135 - 1144
15X-RAY DIFFRACTION15A1145 - 1153
16X-RAY DIFFRACTION16A1154 - 1168
17X-RAY DIFFRACTION17A1169 - 1173
18X-RAY DIFFRACTION18A1174 - 1179
19X-RAY DIFFRACTION19B989 - 996
20X-RAY DIFFRACTION20B997 - 1007
21X-RAY DIFFRACTION21B1008 - 1013
22X-RAY DIFFRACTION22B1014 - 1025
23X-RAY DIFFRACTION23B1026 - 1035
24X-RAY DIFFRACTION24B1036 - 1048
25X-RAY DIFFRACTION25B1049 - 1061
26X-RAY DIFFRACTION26B1062 - 1074
27X-RAY DIFFRACTION27B1075 - 1088
28X-RAY DIFFRACTION28B1089 - 1097
29X-RAY DIFFRACTION29B1098 - 1109
30X-RAY DIFFRACTION30B1110 - 1120
31X-RAY DIFFRACTION31B1121 - 1133
32X-RAY DIFFRACTION32B1134 - 1146
33X-RAY DIFFRACTION33B1147 - 1154
34X-RAY DIFFRACTION34B1155 - 1170
35X-RAY DIFFRACTION35B1171 - 1179
36X-RAY DIFFRACTION36C989 - 998
37X-RAY DIFFRACTION37C999 - 1005
38X-RAY DIFFRACTION38C1006 - 1011
39X-RAY DIFFRACTION39C1012 - 1029
40X-RAY DIFFRACTION40C1030 - 1041
41X-RAY DIFFRACTION41C1042 - 1049
42X-RAY DIFFRACTION42C1050 - 1068
43X-RAY DIFFRACTION43C1069 - 1078
44X-RAY DIFFRACTION44C1079 - 1084
45X-RAY DIFFRACTION45C1085 - 1089
46X-RAY DIFFRACTION46C1090 - 1103
47X-RAY DIFFRACTION47C1104 - 1112
48X-RAY DIFFRACTION48C1113 - 1121
49X-RAY DIFFRACTION49C1122 - 1134
50X-RAY DIFFRACTION50C1135 - 1149
51X-RAY DIFFRACTION51C1150 - 1159
52X-RAY DIFFRACTION52C1160 - 1169
53X-RAY DIFFRACTION53C1170 - 1175
54X-RAY DIFFRACTION54D989 - 1004
55X-RAY DIFFRACTION55D1005 - 1011
56X-RAY DIFFRACTION56D1012 - 1032
57X-RAY DIFFRACTION57D1033 - 1042
58X-RAY DIFFRACTION58D1043 - 1048
59X-RAY DIFFRACTION59D1049 - 1059
60X-RAY DIFFRACTION60D1060 - 1074
61X-RAY DIFFRACTION61D1075 - 1085
62X-RAY DIFFRACTION62D1086 - 1094
63X-RAY DIFFRACTION63D1095 - 1108
64X-RAY DIFFRACTION64D1109 - 1120
65X-RAY DIFFRACTION65D1121 - 1130
66X-RAY DIFFRACTION66D1131 - 1140
67X-RAY DIFFRACTION67D1141 - 1152
68X-RAY DIFFRACTION68D1153 - 1168
69X-RAY DIFFRACTION69D1169 - 1173
70X-RAY DIFFRACTION70D1174 - 1179

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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