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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
All entries (5197)Repr. entries (2266)Latest entries (44)
9GRQ
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BU of 9grq by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
Deposit date:2024-09-12
Release date:2024-09-25
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8WKE
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BU of 8wke by Molmil
Sulfate-bound SARS-CoV-2 Nsp9
Descriptor: Non-structural protein 9, SULFATE ION
Authors:Chen, P.J, Huang, H.Y, Hsiao, W.C, Huang, C.Y.
Deposit date:2023-09-27
Release date:2024-10-02
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:Sulfate-bound SARS-CoV-2 Nsp9
To Be Published
8WSH
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BU of 8wsh by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=4.0
Descriptor: Replicase polyprotein 1ab
Authors:Zhou, X.L, Jiang, H.H, Zhang, J, Li, J.
Deposit date:2023-10-17
Release date:2024-10-02
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Crystal structure of SARS-Cov-2 main protease ,pH=4.0
To Be Published
8WSJ
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BU of 8wsj by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=6.5
Descriptor: 3C-like proteinase nsp5
Authors:Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
Deposit date:2023-10-17
Release date:2024-10-02
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Crystal structure of SARS-Cov-2 main protease, pH=6.5
To Be Published
8WSK
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Crystal structure of SARS-Cov-2 main protease, pH=8.5
Descriptor: 3C-like proteinase nsp5
Authors:Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
Deposit date:2023-10-17
Release date:2024-10-02
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Crystal structure of SARS-Cov-2 main protease, pH=8.5
To Be Published
9CSY
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BU of 9csy by Molmil
SARS-CoV-2 papain-like protease (PLpro) bound to PF-07957472
Descriptor: 2-methyl-5-(4-methylpiperazin-1-yl)-N-{1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]cyclopropyl}benzamide, Papain-like protease, ZINC ION, ...
Authors:Mashalidis, E.H, Chang, J.S, Wu, H, Garnsey, M.
Deposit date:2024-07-24
Release date:2024-10-02
Last modified:2024-10-30
Method:X-RAY DIFFRACTION (2.595 Å)
Cite:Discovery of SARS-CoV-2 papain-like protease (PL pro ) inhibitors with efficacy in a murine infection model.
Sci Adv, 10, 2024
9GTF
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BU of 9gtf by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 57256190
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
Deposit date:2024-09-17
Release date:2024-10-02
Method:X-RAY DIFFRACTION (2.28 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
9GUE
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BU of 9gue by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 57256189
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
Deposit date:2024-09-19
Release date:2024-10-02
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
9GUF
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SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571106
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
Deposit date:2024-09-19
Release date:2024-10-02
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8K18
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Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
Descriptor: Spike protein S1, ZCP4C9 heavy chain, ZCP4C9 light chain
Authors:Bingjie, T, Shangyu, D.
Deposit date:2023-07-10
Release date:2024-10-09
Last modified:2025-06-25
Method:ELECTRON MICROSCOPY (3.68 Å)
Cite:Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
To Be Published
8K19
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Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
Descriptor: Spike protein S1, ZCP3B4 heavy chain, ZCP3B4 light chain
Authors:Tang, B, Dang, S.
Deposit date:2023-07-10
Release date:2024-10-09
Last modified:2025-06-25
Method:ELECTRON MICROSCOPY (3.88 Å)
Cite:Ultrapotent class I neutralizing antibodies post Omicron breakthrough infection overcome broad SARS-CoV-2 escape variants.
Ebiomedicine, 108, 2024
8U4Y
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BU of 8u4y by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F Mutant
Descriptor: 3C-like proteinase nsp5
Authors:Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
Deposit date:2023-09-11
Release date:2024-10-09
Last modified:2025-02-12
Method:X-RAY DIFFRACTION (2.21 Å)
Cite:Distal protein-protein interactions contribute to nirmatrelvir resistance.
Nat Commun, 16, 2025
8WXL
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BU of 8wxl by Molmil
Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state)
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:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2023-10-30
Release date:2024-10-09
Last modified:2024-11-06
Method:ELECTRON MICROSCOPY (2.59 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XUX
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BU of 8xux by Molmil
Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)
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:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-14
Release date:2024-10-09
Last modified:2025-06-18
Method:ELECTRON MICROSCOPY (3.22 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XUY
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BU of 8xuy by Molmil
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-14
Release date:2024-10-09
Last modified:2024-11-20
Method:ELECTRON MICROSCOPY (3.14 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XUZ
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BU of 8xuz by Molmil
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up and 1-down state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-14
Release date:2024-10-09
Last modified:2024-11-06
Method:ELECTRON MICROSCOPY (3.05 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XV0
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BU of 8xv0 by Molmil
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-14
Release date:2024-10-09
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XV1
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Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (down state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-14
Release date:2024-10-09
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (3.05 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XVM
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BU of 8xvm by Molmil
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (3-up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-01-15
Release date:2024-10-09
Last modified:2024-10-23
Method:ELECTRON MICROSCOPY (2.77 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
9IU1
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BU of 9iu1 by Molmil
Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
Deposit date:2024-07-20
Release date:2024-10-09
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (4.3 Å)
Cite:Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8WPW
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BU of 8wpw by Molmil
Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CB6 fab mutant heavy chain, CB6 fab mutant light chain, ...
Authors:Su, C, Qi, J.X, Gao, G.F.
Deposit date:2023-10-10
Release date:2024-10-16
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (2.49 Å)
Cite:An improved design method enables the ineffective etesevimab broadly and efficiently against SARS-CoV-2 Omicron subvariants
To Be Published
8WPY
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BU of 8wpy by Molmil
Cryo-EM structure of SARS-CoV-2 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
Descriptor: CB6 fab mutant heavy chain, CB6 fab mutant light chain, S304 fab heavy chain, ...
Authors:Su, C, Qi, J.X, Gao, G.F.
Deposit date:2023-10-10
Release date:2024-10-16
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.02 Å)
Cite:An improved design method enables the ineffective etesevimab broadly and efficiently against SARS-CoV-2 Omicron subvariants
To Be Published
9ATM
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BU of 9atm by Molmil
SARS-CoV-2 EG.5 RBD bound to the VIR-7229 and the S2H97 Fab fragments
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Rietz, T, Park, Y.J, Errico, J, Czudnochowski, N, Nix, J.C, Corti, D, Snell, G, Marco, A.D, Pinto, D, Cameroni, E, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:2024-02-27
Release date:2024-10-16
Last modified:2024-12-25
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9AU1
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BU of 9au1 by Molmil
SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ...
Authors:Rietz, T, Park, Y.J, Errico, J, Czudnochowski, N, Nix, J.C, Corti, D, Snell, G, Marco, A.D, Pinto, D, Cameroni, E, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D, Structural Genomics Consortium (SGC)
Deposit date:2024-02-27
Release date:2024-10-16
Last modified:2024-12-25
Method:X-RAY DIFFRACTION (2.41 Å)
Cite:A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9AU2
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VIR-7229 Fab fragment bound the BA.2.86 spike trimer (global refinement)
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:Tortorici, M.A, Park, Y.J, Veelser, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2024-02-28
Release date:2024-10-16
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024

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