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coronavirus
Coronavirus, 2020. Modified from the original illustration by David S. Goodsell@RCSB PDB

The recent outbreak of the Novel Coronavirus disease (COVID-19) is a serious threat to people all over the world. In order to understand and develop an effective drug against this virus (Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2), structural work on the related proteins has already started and the resultant entries are accumulating in the PDB. PDBj provides a portal page for the COVID-19 related entries for our users. New entries will be added simultaneously with the public release from the wwPDB.

An explanation article covering one of the proteins of this virus is available on the "Molecules of the Month" page below:

The tab "All entries" contains all PDB IDs, in case you want to check all independent entries, including group depositions by the same authors. The "Repr. entries" tab contains only representative PDB entries with the highest resolution, excluding duplicate entries with 100% amino acid sequence identitiy, even if they contain a different ligand. Finally, the "Latest entries" tab contains the latest entries released this week.


Created: 2020-10-28 (last edited: more than 1 year ago)2022-09-02
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
9JEB
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BU of 9jeb by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv N1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, N1 scFv, Spike protein S1
Authors:Guo, K, Zhang, N, Guo, Y.
Deposit date:2024-09-03
Release date:2025-09-03
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Mining antibody functionality via AI-guided structural landscape profiling
To Be Published
8ZRD
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BU of 8zrd by Molmil
The complex structure of SARS-CoV-2 RBD and llama single-domain antibody S4
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, llama single-domain antibody S4
Authors:Chen, L.
Deposit date:2024-06-04
Release date:2025-09-10
Method:X-RAY DIFFRACTION (2.715 Å)
Cite:Identification of a potent SARS-CoV-2 neutralizing nanobody targeting the receptor-binding domain of the spike protein.
Int.J.Biol.Macromol., 281, 2024
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
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
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
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
9SAR
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BU of 9sar by Molmil
Cryo-EM structure of SARS CoV-2 RdRp wild-type 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 (2.8 Å)
Cite:Structural basis for selective remdesivir incorporation by SARS-CoV-2 RNA polymerase, and S759A resistance.
Biorxiv, 2025
8XZ0
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BU of 8xz0 by Molmil
Crystal complex structure of SARS-CoV-2 S bound to human ezrin
Descriptor: Ezrin, Spike protein S2'
Authors:Wang, J.M, Ma, W.F.
Deposit date:2024-01-20
Release date:2025-10-08
Method:X-RAY DIFFRACTION (2.035 Å)
Cite:Crystal complex structure of SARS-CoV-2 S bound to human ezrin
To Be Published
8XZ4
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BU of 8xz4 by Molmil
SARS-CoV-2 S and radixin complex structure
Descriptor: Radixin, Spike protein S2'
Authors:Wang, J.M, Ma, W.F.
Deposit date:2024-01-20
Release date:2025-10-08
Method:X-RAY DIFFRACTION (2.129 Å)
Cite:SARS-CoV-2 S and radixin complex structure
To Be Published
8XZ5
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BU of 8xz5 by Molmil
SARS-CoV-2 S and moesin complex structure
Descriptor: Moesin, Spike protein S2'
Authors:Wang, J.M, Ma, W.F.
Deposit date:2024-01-20
Release date:2025-10-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 S and moesin complex structure
To Be Published
9C7S
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BU of 9c7s by Molmil
Cryo EM structure of SARS-COV-2 (BQ 1.1) RBD in complex with Fab COV2-3891 (local refine)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab COV-3891 heavy chain, Fab COV-3891 light chain, ...
Authors:Binshtein, E, Crowe, J.E.
Deposit date:2024-06-11
Release date:2025-10-08
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Cryo EM structure of SARS-COV-2 (BQ 1.1) RBD in complex with Fab COV2-3891 (local refine)
To Be Published

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