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- PDB-3suf: Crystal structure of NS3/4A protease variant D168A in complex wit... -

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基本情報

登録情報
データベース: PDB / ID: 3suf
タイトルCrystal structure of NS3/4A protease variant D168A 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 suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / viral nucleocapsid / 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 / induction by virus of host autophagy / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
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, 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 non-structural protein NS2, C-terminal domain / 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, 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 non-structural protein NS2, C-terminal domain / 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 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 zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepatitis C virus, Non-structural protein NS2 / : / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus non-structural 5a protein membrane anchor / 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 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / 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 / 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: 2.19 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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)89,32713
ポリマ－85,9024
非ポリマー3,4259
水2,540141
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)22,3083
ポリマ－21,4751
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
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)22,4044
ポリマ－21,4751
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
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)22,3083
ポリマ－21,4751
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)22,3083
ポリマ－21,4751
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)56.004, 103.560, 73.510
Angle α, β, γ (deg.)90.00, 112.04, 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: 21475.385 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, D1168A
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-ZN / ZINC ION


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


分子量: 18.015 Da / 分子数: 141 / 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: 2.3 Å3/Da / 溶媒含有率: 46.53 %
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: 23-ID-D / 波長: 0.97872 Å
検出器日付: 2011年4月22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, L10.568
11-H, -K, H+L20.432
反射解像度: 2.19→30 Å / Num. obs: 37671 / % possible obs: 95.9 % / 冗長度: 2.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.4
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsDiffraction-ID% possible all
2.19-2.282.70.389194.5
2.28-2.372.70.339195
2.37-2.482.70.29194.8
2.48-2.612.80.246195.4
2.61-2.772.80.193196.3
2.77-2.992.90.134197
2.99-3.2930.104196.7
3.29-3.7630.074196.5
3.76-4.7330.053196.5
4.73-3030.038196.6

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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: 2.19→29.22 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.076 / SU ML: 0.197 / SU R Cruickshank DPI: 0.0624 / 交差検証法: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.05 / 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
Rfree0.25932 1865 5 %RANDOM
Rwork0.19877 ---
obs0.20184 35743 94.35 %-
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: 28.325 Å2
Baniso -1Baniso -2Baniso -3
1-14 Å20 Å2-7.34 Å2
2---2.85 Å20 Å2
3----11.15 Å2
精密化ステップサイクル: LAST / 解像度: 2.19→29.22 Å
タンパク質核酸リガンド溶媒全体
原子数5303 0 225 141 5669
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025640
X-RAY DIFFRACTIONr_bond_other_d0.0080.023572
X-RAY DIFFRACTIONr_angle_refined_deg1.3942.0077755
X-RAY DIFFRACTIONr_angle_other_deg1.3473.0098767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8795746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66222.97165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40615756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6821532
X-RAY DIFFRACTIONr_chiral_restr0.0740.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021082
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_it0.3941.53735
X-RAY DIFFRACTIONr_mcbond_other0.0881.51557
X-RAY DIFFRACTIONr_mcangle_it0.68925990
X-RAY DIFFRACTIONr_scbond_it1.09331905
X-RAY DIFFRACTIONr_scangle_it1.6784.51729
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: 2.19→2.25 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.333 109 -
Rwork0.209 2070 -
obs--73.99 %
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)
12.64630.20490.50312.41170.09040.2814-0.17590.07860.0957-0.36970.0712-0.12170.168-0.13580.10470.2271-0.0449-0.15530.0182-0.0090.26519.6709-6.52970.46
215.45099.2631-2.90024.1826-5.1631.45310.1886-0.98570.2173-0.0169-0.18070.16830.18060.4435-0.0080.315-0.0568-0.17570.1216-0.00910.26053.6624-6.8918-1.345
32.5253-0.8922-2.0687-6.47971.75671.1681-0.1707-0.88180.3840.4866-0.09630.1576-0.2178-0.63330.2670.4029-0.0076-0.12970.31330.00850.3326-2.6148-13.649411.271
4-1.9804-3.0845.01483.00393.1063-2.84530.4642-0.1582-0.63990.0316-0.40990.0649-0.2114-0.1108-0.05430.2556-0.1047-0.22680.1512-0.00660.3398.6347-14.3841.8307
510.4613-4.663-7.0447-0.5259-3.126313.648-0.0157-0.28780.1860.11970.261-0.0261-0.03980.3309-0.24520.2061-0.0181-0.09550.0642-0.03060.22937.5158-5.89887.295
62.7282-0.2744-0.04141.80420.03360.96160.0632-0.0039-0.2320.1102-0.00240.14310.0894-0.0649-0.06080.2161-0.005-0.10120.1130.02540.198211.9987-5.557710.1182
71.0581-1.3125-2.04562.56721.71021.3024-0.06120.03290.03930.0862-0.04280.07650.1132-0.06550.1040.12840.0297-0.07570.12890.00580.168314.0718-4.404315.5263
817.8473-9.9278-4.09179.587812.12672.8967-0.13-0.3637-0.25520.52740.17240.1863-0.1031-0.9283-0.04240.3822-0.0527-0.12510.17940.01250.15417.4316-9.035318.3001
92.55241.60561.20412.06172.18592.0742-0.03010.0894-0.2074-0.2060.198-0.1694-0.0777-0.0751-0.16790.2557-0.0187-0.17030.12770.0390.203912.9256-13.255117.6783
100.6817-1.36051.0248-1.416-1.97861.83490.28870.004-0.0392-0.1959-0.1083-0.12560.0143-0.299-0.18040.2466-0.0198-0.08650.05970.04860.191116.0602-7.503416.7114
11-0.3654-0.8403-0.50330.9290.42570.3971-0.00320.11910.0137-0.09010.04790.0037-0.04790.082-0.04470.1658-0.0476-0.15070.1383-0.00140.26422.7019-3.37693.1168
124.15531.20242.61651.2369-0.14462.8244-0.1423-0.26030.0264-0.01220.148-0.0071-0.0558-0.0988-0.00570.1969-0.0147-0.1060.1106-0.01960.2817.80037.08363.2769
137.8899-2.82211.27680.47351.69413.43070.211-0.1575-0.26160.02630.20140.3902-0.51-0.2992-0.41240.199-0.0595-0.06380.1102-0.01850.267719.660613.50745.9845
142.6241-0.0208-2.32844.8294-0.39064.68670.09770.2157-0.0555-0.09890.00840.2773-0.2314-0.3525-0.10610.1499-0.0017-0.160.1-0.00230.22910.34217.35747.1776
158.73791.9385-5.92111.9497-0.93824.8843-0.1344-0.3238-0.0965-0.22790.1647-0.1964-0.13740.0582-0.03030.15980.0119-0.13280.1026-0.01470.231523.42870.32544.0146
160.46150.09371.432910.9508-1.22-1.7705-0.0661-0.26810.34160.6715-0.0365-0.1279-0.25830.24180.10260.26380.0498-0.14270.2059-0.0220.260414.64814.494512.3069
171.4234-0.82172.4384-0.6549-2.25483.2356-0.0436-0.35320.1262-0.1040.1292-0.23820.2574-0.0189-0.08560.23790.0326-0.13110.137-0.04010.313523.39993.307912.2195
180.8379-1.2246-4.097823.3308-9.56961.88940.24510.1808-0.962-0.3596-0.362-1.1158-0.11741.0440.11690.25420.0702-0.26680.35060.07810.395526.3772-7.180616.7483
190.05140.1732-2.79233.50882.2225-1.2516-0.394-0.03360.09840.25230.313-0.2288-0.02950.14020.0810.1750.0431-0.12050.1294-0.05170.2632-21.656625.615212.1779
200.3802-1.2678-0.05681.727-0.97245.0181-0.1424-0.2783-0.18260.40470.25730.0532-0.09450.1181-0.11490.2005-0.0279-0.14620.1990.09350.3168-21.574523.881319.4479
21-0.3119-1.2088-2.53532.2873-0.8156-0.7077-0.3359-0.08280.1040.37310.40280.0313-0.34970.0813-0.06690.25870.0809-0.18380.110.00260.308-21.58932.07813.0357
223.3546-0.44-1.8768-0.79780.28533.7633-0.1489-0.3737-0.1533-0.0961-0.11790.23010.2028-0.45290.26680.2192-0.0116-0.16180.04840.04360.3668-22.723720.79739.4656
23-3.217-2.8950.5884-1.4519-0.09753.0074-0.08450.1486-0.00950.01920.0767-0.01590.03450.18250.00780.2005-0.0057-0.11290.06480.01760.2414-10.801224.00378.8081
241.4327-0.89741.25951.5942-2.3774-0.6950.16470.1065-0.1214-0.2067-0.08040.12770.1641-0.1229-0.08430.1689-0.0305-0.11390.1070.01240.2874-18.753622.13380.7365
252.4624-0.9301-0.94870.92622.77332.12570.11130.06550.3805-0.1629-0.1595-0.2763-0.3978-0.24890.04820.22910.0316-0.09840.07990.01930.2477-18.338834.32173.2359
265.93113.8943-1.38065.681-4.31743.16830.2101-0.0399-0.0532-0.3348-0.4146-0.1640.24840.02960.20450.1756-0.0168-0.11280.0907-0.00160.2154-9.871320.1341-3.2828
27-0.26640.4188-0.2308-4.1894-1.1511-0.7845-0.15140.02540.13-0.19750.2349-0.3288-0.3207-0.0894-0.08350.2579-0.0528-0.1560.1327-0.03760.3304-12.933929.29175.7183
281.6655-1.59692.0218-0.0957-2.71190.7861-0.1949-0.12240.03710.23230.0649-0.10210.05480.08070.130.24790.079-0.15030.137-0.00580.3338-1.027620.069615.3428
297.163-3.2226-3.89393.95161.43150.4169-0.4455-0.0619-0.68330.3759-0.02440.1312-0.2807-0.34930.46990.30280.0803-0.16230.22010.08180.3056-12.733612.130518.2907
3011.8604-3.4194-14.83683.5984.179213.6859-0.0840.2984-0.08610.0228-0.01770.3513-0.0815-0.18040.10170.17860.0118-0.17260.18920.03570.2186-4.95946.556615.0657
310.91453.02543.60125.8869-0.89720.9331-0.1531-0.2312-0.0636-0.2180.084-0.24860.6214-0.07650.06910.29070.0612-0.1260.14780.01170.2502-9.97743.351411.8688
324.53114.35011.77037.09881.05321.16250.2486-0.0942-0.5660.20450.02020.01840.0549-0.0961-0.26880.16520.0119-0.09810.09250.03370.331-14.576512.099812.8483
332.38541.34974.32193.1431-1.70315.5079-0.2537-0.10490.0588-0.14750.05230.0474-0.31050.0910.20130.15730.0136-0.0690.1721-0.01630.2132-5.902714.580412.0595
3428.549815.0043-5.05785.3637-1.6656-8.4217-0.4241-0.0493-0.2447-0.6631-0.0025-0.3044-0.0148-0.20830.42660.2812-0.0262-0.09060.1383-0.01330.2875-14.375-1.14568.0447
357.89382.04126.44663.19951.8287-2.77070.251-0.110.13120.9336-0.17080.4555-0.14410.1122-0.08020.3284-0.069-0.04490.1001-0.00760.1941-5.486812.89256.3453
368.1178-3.9359-2.92697.98112.74727.0632-0.0746-0.41860.1529-0.2001-0.101-0.9124-0.2372-0.09210.17560.1656-0.0427-0.11150.0619-0.00040.2836-1.126922.20372.0051
373.37571.34620.34790.16891.7893-2.78410.13830.05040.1866-0.08570.08660.07790.25480.2796-0.22490.19550.0552-0.10790.0667-0.01140.23851.773-6.8127-16.1821
38-2.874311.2062-5.11275.9011-1.45675.37140.1506-0.6307-0.3340.1045-0.1046-0.1207-0.3232-0.2522-0.0460.2593-0.0142-0.22420.37420.10780.3101-6.2861-10.194-2.5679
3914.85422.4889-6.40995.43854.81879.86290.30250.8317-0.21360.0893-0.2469-0.1388-0.5131-0.3486-0.05570.15940.0576-0.17410.11240.04890.22615.9458-6.3479-10.0434
406.80811.71720.05271.1572-1.7246-0.631-0.0076-0.1236-0.0865-0.1039-0.1131-0.3064-0.0090.1940.12070.3070.046-0.09360.11840.01480.29958.2963-8.6835-18.3012
41-0.7864-2.3262-4.513418.2993-1.44726.874-0.36170.1158-0.1047-0.01440.2780.04730.0581-0.46920.08370.10250.0129-0.15860.11880.06190.2256-3.7283-8.6816-13.5863
420.72684.4706-0.176612.52713.8767-6.56650.1584-0.50780.0511-0.1396-0.1435-0.3272-0.19060.5777-0.01490.2097-0.0801-0.10630.2890.01610.30320.44931.9429-19.4721
431.45020.6960.17090.06540.49740.0609-0.0174-0.0223-0.04050.14840.0404-0.26270.081-0.129-0.02310.22950.016-0.10660.0819-0.01290.217-7.9482-7.1285-22.2998
44-0.10211.05922.06361.11071.29990.4487-0.12550.0805-0.0221-0.0880.1908-0.0909-0.0210.2008-0.06530.23540.0574-0.13420.1863-0.00390.23810.7795-10.7566-27.5303
455.2706-2.28981.75724.6343-1.77162.40740.15360.161-0.1949-0.1742-0.1090.16180.11330.0481-0.04460.22160.0213-0.1170.0946-0.01770.1809-8.9654-7.1488-27.1652
461.6058-0.03830.81360.56310.74221.22230.0211-0.4175-0.02020.2532-0.0757-0.00580.118-0.04560.05460.2585-0.0748-0.1260.16630.0210.2267-14.1535-9.5188-10.5758
47-1.027-0.5625-4.8432.7513-0.2254-1.1738-0.0394-0.4139-0.1192-0.1742-0.20460.0105-0.7205-0.44630.24410.25430.0199-0.16550.115-0.01420.2288-21.9139-2.2294-8.3639
484.00891.53866.11671.89212.1522.50260.20110.2393-0.19310.09420.00030.2620.251-0.0715-0.20140.2225-0.0695-0.12850.19720.03150.2308-23.41341.2632-11.6714
490.4925-4.0055-0.50133.98112.2315-1.9486-0.2606-0.4567-0.08250.22620.1966-0.13850.17240.0120.0640.2636-0.0462-0.12910.16170.01210.2124-11.65957.4644-8.4943
50-1.48610.20890.33842.77640.2073-2.7998-0.11640.25630.00570.03870.24070.11760.1813-0.1331-0.12430.3068-0.0801-0.15090.20310.01850.2589-15.1504-7.759-10.9827
512.01390.4864-1.872411.4722-3.44921.5572-0.1857-0.02090.0802-0.5190.318-0.07760.1442-0.264-0.13230.20840.0039-0.18290.09640.00580.2276-16.8916-2.2191-15.9257
521.6728-0.25260.8819-7.3791-3.9568-1.27440.0482-0.02930.1211-0.06780.06470.2508-0.2532-0.0354-0.11290.2237-0.0342-0.06870.1216-0.02820.271-19.00773.207-15.05
53-4.6669-0.0155.6187-1.49712.80662.26830.06020.2551-0.2302-0.3541-0.0869-0.11840.47390.18110.02670.48720.0016-0.0650.1846-0.10710.3838-18.3595-13.332-26.9153
54-0.88292.7852-3.8230.22850.4312-1.6149-0.3596-0.1050.18130.18640.0722-0.1002-0.3224-0.19990.28750.2951-0.0106-0.19620.2204-0.03510.29640.688822.5724-34.4999
55-0.2042.5286-2.86440.83592.38540.495-0.13690.17360.3123-0.05080.0452-0.045-0.07780.02970.09170.3293-0.0936-0.14080.18590.06360.3415-0.828924.2182-43.927
56-0.6513-0.2666-3.46131.44640.2768-1.90070.14260.10240.0565-0.1509-0.2474-0.23640.30740.45220.10480.2859-0.0084-0.22370.30220.00510.38448.983122.3474-29.6975
572.14-2.69950.63219.4537-5.19657.79670.0030.2836-0.12260.3006-0.24830.02660.01061.09660.24530.2471-0.1008-0.12950.1127-0.05140.36110.216317.0628-31.6619
58-4.50126.89461.86713.26634.35187.85630.37350.23760.0851-0.6667-0.59160.243-0.1280.4110.21820.3179-0.0058-0.11060.13460.00330.259-6.715223.1394-31.3682
591.1237-1.1860.82220.7336-0.00031.8720.2180.13870.34780.2612-0.3231-0.0655-0.08850.17220.10510.2412-0.049-0.13960.0811-0.0090.2593-7.279520.7059-25.4694
601.8368-4.3901-0.60641.78460.3666-1.29120.13480.12980.27720.099-0.13780.1418-0.05490.530.0030.3282-0.1091-0.20470.374-0.0070.23712.719124.5416-21.5991
61-2.74280.33482.94560.11562.8918.02640.0047-0.1689-0.0907-0.02550.24650.101-0.1189-0.121-0.25120.2616-0.017-0.12670.10030.03010.2503-11.767719.9706-19.8916
627.25621.1434.34460.4390.32542.73620.08690.32270.19370.0278-0.0901-0.09480.41970.59010.00320.3768-0.0507-0.16850.15380.01530.3723-4.797529.7831-28.3298
632.5899-0.87282.63824.7229-1.4122-0.74220.06430.17350.16490.27490.00650.29540.0494-0.2491-0.07080.31860.0328-0.0660.12860.030.2671-21.443826.7633-37.9614
64-1.15842.54370.05531.9611-2.3142.6134-0.06350.2505-0.1337-0.0068-0.0686-0.1741-0.06440.01760.13210.27650.0037-0.09750.0851-0.03230.2193-15.791917.7043-41.4081
65-1.30161.45015.975811.98634.79821.56170.0861-0.3428-0.68130.5864-0.42780.41270.1139-0.08750.34170.2088-0.0575-0.12510.17090.0510.3381-23.471614.9408-36.7248
662.20844.19662.04742.59973.10796.96830.03480.26030.1531-0.0862-0.0587-0.0316-0.12820.10790.02390.24930.0442-0.11530.12490.00560.2088-11.200710.202-39.0446
6713.01261.1677-4.36342.0816-6.2538.922-0.02630.2016-0.0740.1822-0.0760.18930.50820.0550.10230.3288-0.0099-0.09970.0219-0.0650.2384-16.949326.4619-39.2623
681.19333.71420.28522.30030.03582.76650.0168-0.1542-0.02070.37780.0338-0.1361-0.0865-0.2778-0.05050.15420.0207-0.08560.1064-0.0030.2444-16.566118.0182-32.8957
69-0.5481-1.83441.412112.96412.23363.47820.00920.09230.0727-0.1768-0.540.9204-0.077-0.53440.53080.15780.0021-0.07650.072-0.05670.2523-19.207110.9253-34.5638
70-4.3622.3548-2.8085-9.18940.829721.2924-0.0354-0.27020.15050.15-0.44940.36980.2114-0.41470.48470.3580.0532-0.14130.1593-0.0590.3372-17.224327.4565-23.2765
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A990 - 1005
2X-RAY DIFFRACTION2A1006 - 1012
3X-RAY DIFFRACTION3A1013 - 1024
4X-RAY DIFFRACTION4A1025 - 1032
5X-RAY DIFFRACTION5A1033 - 1038
6X-RAY DIFFRACTION6A1039 - 1051
7X-RAY DIFFRACTION7A1052 - 1057
8X-RAY DIFFRACTION8A1058 - 1064
9X-RAY DIFFRACTION9A1065 - 1079
10X-RAY DIFFRACTION10A1080 - 1086
11X-RAY DIFFRACTION11A1087 - 1108
12X-RAY DIFFRACTION12A1109 - 1121
13X-RAY DIFFRACTION13A1122 - 1130
14X-RAY DIFFRACTION14A1131 - 1142
15X-RAY DIFFRACTION15A1143 - 1154
16X-RAY DIFFRACTION16A1155 - 1165
17X-RAY DIFFRACTION17A1166 - 1173
18X-RAY DIFFRACTION18A1174 - 1179
19X-RAY DIFFRACTION19B990 - 998
20X-RAY DIFFRACTION20B999 - 1019
21X-RAY DIFFRACTION21B1020 - 1032
22X-RAY DIFFRACTION22B1033 - 1042
23X-RAY DIFFRACTION23B1043 - 1053
24X-RAY DIFFRACTION24B1054 - 1064
25X-RAY DIFFRACTION25B1065 - 1074
26X-RAY DIFFRACTION26B1075 - 1081
27X-RAY DIFFRACTION27B1082 - 1089
28X-RAY DIFFRACTION28B1090 - 1103
29X-RAY DIFFRACTION29B1104 - 1112
30X-RAY DIFFRACTION30B1113 - 1119
31X-RAY DIFFRACTION31B1120 - 1133
32X-RAY DIFFRACTION32B1134 - 1144
33X-RAY DIFFRACTION33B1145 - 1157
34X-RAY DIFFRACTION34B1158 - 1166
35X-RAY DIFFRACTION35B1167 - 1172
36X-RAY DIFFRACTION36B1173 - 1179
37X-RAY DIFFRACTION37C990 - 998
38X-RAY DIFFRACTION38C999 - 1007
39X-RAY DIFFRACTION39C1008 - 1012
40X-RAY DIFFRACTION40C1013 - 1031
41X-RAY DIFFRACTION41C1032 - 1036
42X-RAY DIFFRACTION42C1037 - 1043
43X-RAY DIFFRACTION43C1044 - 1061
44X-RAY DIFFRACTION44C1062 - 1075
45X-RAY DIFFRACTION45C1076 - 1088
46X-RAY DIFFRACTION46C1089 - 1112
47X-RAY DIFFRACTION47C1113 - 1119
48X-RAY DIFFRACTION48C1120 - 1128
49X-RAY DIFFRACTION49C1129 - 1137
50X-RAY DIFFRACTION50C1138 - 1148
51X-RAY DIFFRACTION51C1149 - 1159
52X-RAY DIFFRACTION52C1160 - 1172
53X-RAY DIFFRACTION53C1173 - 1179
54X-RAY DIFFRACTION54D990 - 1000
55X-RAY DIFFRACTION55D1001 - 1012
56X-RAY DIFFRACTION56D1014 - 1032
57X-RAY DIFFRACTION57D1033 - 1041
58X-RAY DIFFRACTION58D1042 - 1049
59X-RAY DIFFRACTION59D1050 - 1059
60X-RAY DIFFRACTION60D1060 - 1074
61X-RAY DIFFRACTION61D1075 - 1083
62X-RAY DIFFRACTION62D1084 - 1094
63X-RAY DIFFRACTION63D1095 - 1106
64X-RAY DIFFRACTION64D1107 - 1119
65X-RAY DIFFRACTION65D1120 - 1128
66X-RAY DIFFRACTION66D1129 - 1141
67X-RAY DIFFRACTION67D1142 - 1148
68X-RAY DIFFRACTION68D1149 - 1159
69X-RAY DIFFRACTION69D1160 - 1171
70X-RAY DIFFRACTION70D1172 - 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