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COVID-19特辑

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冠状病毒
冠状病毒,2020. 由David S. Goodsell @ RCSB PDB原图修改

最近爆发的新型冠状病毒传染病(Novel Coronavirus disease 2019: COVID-19)对全世界的人们都构成了严重威胁。 为了尽早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以开发出有效的抗病毒药物,已经有很多科研人員开始了相关蛋白结构的研究,并且将所获得的结构数据存储于PDB。 PDBj为用户提供了COVID-19相关数据一览的门户页面,并将于每周三更新当日新发布的相关数据。

有关该病毒蛋白质的解说,请参见下面的“当月的分子”页面。

“所有结构”标签的页面则逐一罗列了所有的结构数据,包括由同一研究组提交的系列数据群。 “代表性结构”标签的页面精选具有相同氨基酸序列的结构数据中的高分辨率数据,不重复选择具同一氨基酸序列的数据,即使该数据可能包含不同配体。 “最新条目”标签内包含本周新更新数据。


Created: 2020-09-03 (last edited: more than 1 year ago)2020-12-02
7IJH
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BU of 7ijh by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8990523176
Descriptor: (3S)-3-[(5-methyl-7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]-3-phenylpropanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJI
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BU of 7iji by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8990523172
Descriptor: (3S)-3-[(2-methyl-7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]-3-phenylpropanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJJ
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BU of 7ijj by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8990919037
Descriptor: (3R)-3-(3-hydroxyphenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, (3S)-3-(3-hydroxyphenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, ...
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (0.98 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJK
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BU of 7ijk by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8990919048
Descriptor: (2R,3S)-2-hydroxy-3-phenyl-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (0.98 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJL
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BU of 7ijl by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8990523194
Descriptor: (3S)-3-[(2-chloro-7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]-3-phenylpropanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJM
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BU of 7ijm by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z7534253453
Descriptor: (3S)-3-phenyl-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
9PYS
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BU of 9pys by Molmil
NMR RDC refinement of the helical domain of the SARS-CoV-2 monomeric Main Protease (MPROH41Q,10-306)
Descriptor: 3C-like proteinase nsp5
Authors:Smith, M.J, Ying, J, Shen, Y, Louis, J.M, Bax, A.
Deposit date:2025-08-08
Release date:2025-09-17
Method:SOLUTION NMR
Cite:Solution Domain Dynamics of Monomeric SARS-CoV-2 Main Protease Revealed by Optimized NMR Residual Dipolar Coupling Measurements.
To Be Published
9PYT
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BU of 9pyt by Molmil
NMR RDC refinement of the catalytic domain of the SARS-CoV-2 monomeric Main Protease (MPROH41Q,10-306)
Descriptor: 3C-like proteinase nsp5
Authors:Smith, M.J, Ying, J, Shen, Y, Louis, J.M, Bax, A.
Deposit date:2025-08-08
Release date:2025-09-17
Method:SOLUTION NMR
Cite:Solution Domain Dynamics of Monomeric SARS-CoV-2 Main Pro-tease Revealed by Optimized NMR Residual Dipolar Coupling Measurements.
To Be Published
9PYW
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BU of 9pyw by Molmil
SARS-CoV-2 nsp7, nsp8 and nsp12 bound to a primer-template pair with incorporated ara-UMP
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Xiao, Z, Kirchdeorfer, R.N.
Deposit date:2025-08-08
Release date:2025-09-17
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:The 2'-endo conformation of arabinose-CTP and arabinose-UTP inhibit viral polymerases by inducing long pauses.
Biorxiv, 2025
9PYZ
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BU of 9pyz by Molmil
SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Xiao, Z, Kirchdeorfer, R.N.
Deposit date:2025-08-08
Release date:2025-09-17
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:The 2'-endo conformation of arabinose-CTP and arabinose-UTP inhibit viral polymerases by inducing long pauses.
Biorxiv, 2025
9PZ0
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BU of 9pz0 by Molmil
SARS-CoV-2 core polymerase complex with two UTP incorporation
Descriptor: Non-structural protein 7, Non-structural protein 8, Primer RNA, ...
Authors:Xiao, Z, Kirchdeorfer, R.N.
Deposit date:2025-08-08
Release date:2025-09-17
Method:ELECTRON MICROSCOPY (3 Å)
Cite:The 2'-endo conformation of arabinose-CTP and arabinose-UTP inhibit viral polymerases by inducing long pauses.
Biorxiv, 2025
9WHE
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BU of 9whe by Molmil
A novel, covalent and highly synthetically accessible SARS-CoV-2 Mpro chloroacetamide inhibitor
Descriptor: (2~{R})-~{N}-[4,4-bis(fluoranyl)cyclohexyl]-2-[ethanoyl-[4-(1,2-thiazol-5-yl)phenyl]amino]-2-pyrazin-2-yl-ethanamide, 1,2-ETHANEDIOL, 3C-like proteinase, ...
Authors:Zagribelnyy, B, Zhavoronkov, A.
Deposit date:2025-08-26
Release date:2025-09-17
Last modified:2025-10-15
Method:X-RAY DIFFRACTION (1.82 Å)
Cite:A novel, covalent and highly synthetically accessible SARS-CoV-2 Mpro chloroacetamide inhibitor
To Be Published
9MDQ
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BU of 9mdq by Molmil
Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) Complex with Azapeptide Inhibitor 20a
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-{2-(dichloroacetyl)-2-[(2-oxo-1,2-dihydropyridin-3-yl)methyl]hydrazin-1-yl}-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Vishwakarma, J, Taylor, A.B, Harris, R.S.
Deposit date:2024-12-05
Release date:2025-09-24
Last modified:2025-10-08
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Azapeptide-Based SARS-CoV-2 Main Protease Inhibitors: Design, Synthesis, Enzyme Inhibition, Structural Determination, and Antiviral Activity.
J.Med.Chem., 68, 2025
9Q1J
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BU of 9q1j by Molmil
Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 E191A mutant-T20P14-R complex
Descriptor: MAGNESIUM ION, Non-structural protein 10, Proofreading exoribonuclease, ...
Authors:Yang, Y, Liu, C, Liu, B.
Deposit date:2025-08-14
Release date:2025-09-24
Last modified:2025-10-15
Method:ELECTRON MICROSCOPY (2.81 Å)
Cite:Molecular basis of SARS-CoV-2 proofreading enzyme-mediated resistance to remdesivir.
Proc.Natl.Acad.Sci.USA, 122, 2025
9VS1
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BU of 9vs1 by Molmil
Crystal structure of SARS-CoV-2 3CL protease in complex with compound 15
Descriptor: 1,2-ETHANEDIOL, 3C-like proteinase, 4-chloranyl-3-[6-methyl-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-2,4,5-tris(oxidanylidene)-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrido[4,3-d]pyrimidin-7-yl]benzenecarbonitrile
Authors:Yamamoto, S, Taoda, Y.
Deposit date:2025-07-08
Release date:2025-09-24
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Design, synthesis and biological evaluation of novel quinazolinedione derivatives as non-covalent SARS-CoV-2 3CL protease inhibitors.
Bioorg.Med.Chem.Lett., 129, 2025
8YUB
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BU of 8yub by Molmil
Crystal structure of SARS-CoV-2 ConSp RBD in complex with neutralizing antibody CC25.4 Fab
Descriptor: 1,2-ETHANEDIOL, Neutralizing antibody CC25.4 heavy chain, Neutralizing antibody CC25.4 light chain, ...
Authors:Kang, J.M, Yuan, M, Han, B.W, Wilson, I.A.
Deposit date:2024-03-27
Release date:2025-10-01
Method:X-RAY DIFFRACTION (2.49 Å)
Cite:Structure and antigenic characteristics of consensus sequence-based SARS-CoV-2 antigen
To Be Published
8YUC
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BU of 8yuc by Molmil
Crystal structure of SARS-CoV-2 ConSp RBD in complex with antibodies PDI222 Fab and COVA1-16 Fab
Descriptor: COVA1-16 heavy chain, COVA1-16 light chain, PDI222 heavy chain, ...
Authors:Kang, J.M, Yuan, M, Han, B.W, Wilson, I.A.
Deposit date:2024-03-27
Release date:2025-10-01
Method:X-RAY DIFFRACTION (4.51 Å)
Cite:Structure and antigenic characteristics of consensus sequence-based SARS-CoV-2 antigen
To Be Published
9BF7
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BU of 9bf7 by Molmil
SARS-CoV-2 Papain-like Protease (PLpro) C111S Untagged Crystal Structure
Descriptor: ACETATE ION, GLYCEROL, PHOSPHATE ION, ...
Authors:Al-Homoudi, A.I, Brunzelle, J.S, Gavande, N, Kovari, L.C.
Deposit date:2024-04-17
Release date:2025-10-01
Last modified:2025-10-15
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Human Structural Homologues of SARS-CoV-2 PL pro as Anti-Targets: A Strategic Panel Analysis.
MicroPubl Biol, 2025, 2025
9OG4
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BU of 9og4 by Molmil
SARS-COV-2-6P-MUT7 S PROTEIN-DY-III-281 complex closed conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Chandravanshi, M, Niu, L, Tolbert, W.D, Pazgier, M.
Deposit date:2025-04-30
Release date:2025-10-01
Method:ELECTRON MICROSCOPY (3.56 Å)
Cite:Optimization of VE607 to generate analogs with improved neutralization activities against SARS-CoV-2 variants
J.Virol., 2025
9OG5
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BU of 9og5 by Molmil
SARS-COV-2-6P-MUT7 S PROTEIN-DY-III-281 complex 1 RBD up conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Chandravanshi, M, Niu, L, Tolbert, W.D, Pazgier, M.
Deposit date:2025-04-30
Release date:2025-10-01
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Optimization of VE607 to generate analogs with improved neutralization activities against SARS-CoV-2 variants
J.Virol., 2025
9OG6
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BU of 9og6 by Molmil
Apo SARS-COV-2-6P-MUT7 S PROTEIN closed conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Niu, L, Chandravanshi, M, Tolbert, W.D, Pazgier, M.
Deposit date:2025-04-30
Release date:2025-10-01
Method:ELECTRON MICROSCOPY (3.14 Å)
Cite:Optimization of VE607 to generate analogs with improved neutralization activities against SARS-CoV-2 variants
J.Virol., 2025
9OG7
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BU of 9og7 by Molmil
APO SARS-COV-2-6P-MUT7 S PROTEIN 1 RBD UP CONFORMATION
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Niu, L, Chandravanshi, M, Tolbert, W.D, Pazgier, M.
Deposit date:2025-04-30
Release date:2025-10-01
Method:ELECTRON MICROSCOPY (3.09 Å)
Cite:Optimization of VE607 to generate analogs with improved neutralization activities against SARS-CoV-2 variants
J.Virol., 2025
9SAO
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BU of 9sao by Molmil
Cryo-EM structure of SARS CoV-2 RdRp S759A mutant in complex with 20-40mer RNA incorporating remdesivir
Descriptor: Non-structural protein 7, Non-structural protein 8, RNA primer strand (25-MER), ...
Authors:Oliva, M.F, Das, K.
Deposit date:2025-08-07
Release date:2025-10-01
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural basis for selective remdesivir incorporation by SARS-CoV-2 RNA polymerase, and S759A resistance.
Biorxiv, 2025
9SAP
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BU of 9sap by Molmil
Cryo-EM structure of SARS CoV-2 RdRp wild-type in complex with 20-40mer RNA incorporating Remdesivir
Descriptor: Non-structural protein 7, Non-structural protein 8, RNA primer strand (25-MER), ...
Authors:Oliva, M.F, Das, K.
Deposit date:2025-08-07
Release date:2025-10-01
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural basis for selective remdesivir incorporation by SARS-CoV-2 RNA polymerase, and S759A resistance.
Biorxiv, 2025
9SAQ
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BU of 9saq by Molmil
Cryo-EM structure of SARS CoV-2 RdRp S759A mutant in complex with 20-40mer RNA incorporating ATP
Descriptor: Non-structural protein 7, Non-structural protein 8, RNA primer strand (27-MER), ...
Authors:Oliva, M.F, Das, K.
Deposit date:2025-08-07
Release date:2025-10-01
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Structural basis for selective remdesivir incorporation by SARS-CoV-2 RNA polymerase, and S759A resistance.
Biorxiv, 2025

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数据于2025-10-22公开中

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