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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
7HQP
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BU of 7hqp by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with CACHE3HI_1715_9
Descriptor: 4-[(3R)-3-(2-fluorophenyl)pyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-12-08
Release date:2025-08-20
Method:X-RAY DIFFRACTION (0.99 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
9ECZ
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BU of 9ecz by Molmil
Cryo-EM structure of SARS-CoV-2 spike protein in complex with human neutralizing antibody WRAIR-2008 (focused refinement of NTD and WRAIR-2008)
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:Jensen, J.L, Thomas, P.V, Joyce, M.G.
Deposit date:2024-11-15
Release date:2025-08-20
Last modified:2025-10-22
Method:ELECTRON MICROSCOPY (3.89 Å)
Cite:First-generation N-terminal domain supersite public antibodies retain activity against Omicron-derived lineages and protect mice against Omicron BA.5 challenge.
Mbio, 16, 2025
9FWK
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BU of 9fwk by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00123
Descriptor: (4R)-4-pyridin-4-ylpyrrolidin-2-one, (4S)-4-pyridin-4-ylpyrrolidin-2-one, DIMETHYL SULFOXIDE, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.509 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00123
To Be Published
9IMK
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BU of 9imk by Molmil
SARS-CoV-2 Replication-Transcription Complex has a dimer architecture (dRTC) in post-capping state
Descriptor: Helicase nsp13, Non-structural protein 7, Non-structural protein 8, ...
Authors:Yan, L.M, Rao, Z.H, Lou, Z.Y.
Deposit date:2024-07-03
Release date:2025-08-20
Method:ELECTRON MICROSCOPY (4.01 Å)
Cite:Structural basis for concurrence of template recycling and RNA capping in SARS-CoV-2 replication/transcription
To Be Published
9IMM
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BU of 9imm by Molmil
SARS-CoV-2 Replication-Transcription Complex has a dimer architecture (local dRTC) in post-capping state
Descriptor: Helicase nsp13, Non-structural protein 7, Non-structural protein 8, ...
Authors:Yan, L.M, Rao, Z.H, Lou, Z.Y.
Deposit date:2024-07-03
Release date:2025-08-20
Method:ELECTRON MICROSCOPY (3.22 Å)
Cite:Structural basis for the concurrence of template recycling and RNA capping in SARS-CoV-2
To Be Published
9KGJ
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BU of 9kgj by Molmil
Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity
Descriptor: (S)-3-((S)-3-cyclobutyl-2-((R)-2-cyclopentyl-N-methyl-2-pivalamidoacetamido)propanamido)-N-cyclopropyl-2-oxo-4-((S)-2-oxopiperidin-3-yl)butanamide, 3C-like proteinase nsp5, cyclopropylcarbamic acid
Authors:Baburajendran, N.
Deposit date:2024-11-08
Release date:2025-08-20
Last modified:2025-09-10
Method:X-RAY DIFFRACTION (1.37 Å)
Cite:Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 M pro Inhibitor with Pan-Coronavirus Activity.
J.Med.Chem., 68, 2025
9KGN
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BU of 9kgn by Molmil
Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity
Descriptor: 3C-like proteinase nsp5, compound 3
Authors:Baburajendran, N.
Deposit date:2024-11-08
Release date:2025-08-20
Last modified:2025-09-10
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 M pro Inhibitor with Pan-Coronavirus Activity.
J.Med.Chem., 68, 2025
9KGQ
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BU of 9kgq by Molmil
Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity
Descriptor: 3C-like proteinase nsp5, compound 4
Authors:Baburajendran, N.
Deposit date:2024-11-08
Release date:2025-08-20
Last modified:2025-09-10
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 M pro Inhibitor with Pan-Coronavirus Activity.
J.Med.Chem., 68, 2025
9KGR
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BU of 9kgr by Molmil
Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity
Descriptor: (S)-2-((R)-2-cyclopentyl-2-pivalamidoacetamido)-N-((2S,3R)-4-(cyclopropylamino)-3-hydroxy-4-oxo-1-((S)-2-oxopiperidin-3-yl)butan-2-yl)pentanamide, 3C-like proteinase nsp5, cyclopropylcarbamic acid
Authors:Baburajendran, N.
Deposit date:2024-11-08
Release date:2025-08-20
Last modified:2025-09-10
Method:X-RAY DIFFRACTION (1.47 Å)
Cite:Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 M pro Inhibitor with Pan-Coronavirus Activity.
J.Med.Chem., 68, 2025
9KGS
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BU of 9kgs by Molmil
Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity
Descriptor: (S)-2-((R)-2-cyclopentyl-N-methyl-2-pivalamidoacetamido)-N-((S)-1-imino-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)pentanamide, 3C-like proteinase nsp5, cyclopropylcarbamic acid
Authors:Baburajendran, N.
Deposit date:2024-11-09
Release date:2025-08-20
Last modified:2025-09-10
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Discovery of an Orally Bioavailable Reversible Covalent SARS-CoV-2 M pro Inhibitor with Pan-Coronavirus Activity.
J.Med.Chem., 68, 2025
9KVD
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BU of 9kvd by Molmil
Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, The heavy chain of 3G5, ...
Authors:Sun, H, Jiang, Y, Wang, S, Zheng, Z, Li, S, Zheng, Q.
Deposit date:2024-12-05
Release date:2025-08-20
Method:ELECTRON MICROSCOPY (3.44 Å)
Cite:Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11
To Be Published
9KVE
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BU of 9kve by Molmil
Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1
Descriptor: Spike protein S1, The heavy chain of 4A5, The heavy chain of 4C1, ...
Authors:Sun, H, Jiang, Y, Wang, S, Zheng, Z, Li, S, Zheng, Q.
Deposit date:2024-12-05
Release date:2025-08-20
Method:ELECTRON MICROSCOPY (2.98 Å)
Cite:Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1
To Be Published
9KVF
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BU of 9kvf by Molmil
Cryo-EM structure of SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10
Descriptor: 2E10 heavy chain, 2E10 light chain, 4A5 heavy chain, ...
Authors:Sun, H, Jiang, Y, Wang, S, Zheng, Z, Li, S, Zheng, Q.
Deposit date:2024-12-05
Release date:2025-08-20
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Cryo-EM structure of SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10
To Be Published
9MI3
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BU of 9mi3 by Molmil
Cryo-EM structure of SARS-CoV-2 spike protein in complex with neutralizing human antibody WRAIR-2008
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, WRAIR-2008 antibody Fab heavy chain, ...
Authors:Jensen, J.L, Thomas, P.V, Joyce, M.G.
Deposit date:2024-12-12
Release date:2025-08-20
Last modified:2025-10-22
Method:ELECTRON MICROSCOPY (3.23 Å)
Cite:First-generation N-terminal domain supersite public antibodies retain activity against Omicron-derived lineages and protect mice against Omicron BA.5 challenge.
Mbio, 16, 2025
9N3M
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BU of 9n3m by Molmil
SARS-CoV-2 Mpro L50F/E166A/L167F triple mutant bound to inhibitor
Descriptor: (1S,2S,4S)-2-{[3-cyclopropyl-N-(4-methoxy-1H-indole-2-carbonyl)-L-alanyl]amino}-1-hydroxy-4-methyl-5-(methylamino)-5-oxopentane-1-sulfonic acid, 3C-like proteinase
Authors:Lu, J, Chen, P, Demmon, S, Fischer, C, Vederas, J.C, Lemieux, M.J.
Deposit date:2025-01-31
Release date:2025-08-20
Last modified:2025-09-03
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structural insights into the nirmatrelvir-resistant SARS-CoV-2 M pro L50F/E166A/L167F triple mutant-inhibitor-complex reveal strategies for next generation coronaviral inhibitor design.
Rsc Med Chem, 2025
9UCN
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BU of 9ucn by Molmil
Monomer of SARS-CoV-2 nsp4CTD
Descriptor: Non-structural protein 4
Authors:Meng, L, Pei, K, Tang, C.
Deposit date:2025-04-04
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.44 Å)
Cite:Structural Dynamics of SARS-CoV-2 NSP4 C-terminal Domain and Implications for Viral Processing.
J.Mol.Biol., 437, 2025
9ATQ
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BU of 9atq by Molmil
XBB.1.5 spike/Nanosota-8 complex
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:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2024-02-27
Release date:2025-08-27
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Structure of XBB.1.5 spike and Nanosota-8 complex
To Be Published
9ATR
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BU of 9atr by Molmil
local refinement of XBB.1.5 spike/Nanosota-8 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-8, ...
Authors:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2024-02-27
Release date:2025-08-27
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Structure of XBB.1.5 spike and Nanosota-3C complex
To Be Published
9BND
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BU of 9bnd by Molmil
SARS-CoV-2 spike HexaPro protein in complex with T0A trimeric antagonist
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2, ...
Authors:Young, T.
Deposit date:2024-05-02
Release date:2025-08-27
Method:ELECTRON MICROSCOPY (3.19 Å)
Cite:Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal COVID antagonist
To Be Published
9BNE
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BU of 9bne by Molmil
SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2, ...
Authors:Young, T.
Deposit date:2024-05-02
Release date:2025-08-27
Method:ELECTRON MICROSCOPY (3.43 Å)
Cite:Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal COVID antagonist
To Be Published
9BNF
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BU of 9bnf by Molmil
SARS-CoV-2 spike HexaPro protein in complex with T5A trimeric antagonist
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2, ...
Authors:Young, T.
Deposit date:2024-05-02
Release date:2025-08-27
Method:ELECTRON MICROSCOPY (3.33 Å)
Cite:Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal COVID antagonist
To Be Published
9BNG
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BU of 9bng by Molmil
SARS-CoV-2 spike HexaPro protein in complex with T18A trimeric antagonist
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Collagen alpha-1(XVIII) chain,Processed angiotensin-converting enzyme 2, ...
Authors:Young, T.
Deposit date:2024-05-02
Release date:2025-08-27
Method:ELECTRON MICROSCOPY (3.73 Å)
Cite:Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal COVID antagonist
To Be Published
9GHN
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BU of 9ghn by Molmil
Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of Q256A
Descriptor: 1,2-ETHANEDIOL, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Creon, A, Scheer, T.E.S, Lane, T.J, Rahmani Mashhour, A, Guenther, S, Reinke, P.Y.A, Meents, A, Chapman, H.N.
Deposit date:2024-08-15
Release date:2025-09-03
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of Q256A
To Be Published
9GHO
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BU of 9gho by Molmil
Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of S284A
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE
Authors:Creon, A, Scheer, T.E.S, Lane, T.J, Rahmani Mashhour, A, Guenther, S, Reinke, P.Y.A, Meents, A, Chapman, H.N.
Deposit date:2024-08-15
Release date:2025-09-03
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of S284A
To Be Published
9GI6
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BU of 9gi6 by Molmil
Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of N214A
Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, Replicase polyprotein 1a, ...
Authors:Creon, A, Scheer, T.E.S, Lane, T.J, Rahmani Mashhour, A, Guenther, S, Reinke, P.Y.A, Meents, A, Chapman, H.N.
Deposit date:2024-08-17
Release date:2025-09-03
Method:X-RAY DIFFRACTION (1.83 Å)
Cite:Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of N214A
To Be Published

243531

数据于2025-10-22公开中

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