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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 (4124)Repr. entries (1833)Latest entries (15)
8J3B
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Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Lin, C, Zou, X.F, Zhang, J, Li, J.
Deposit date:2023-04-16
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.64 Å)
Cite:Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF00835231
To Be Published
8J39
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Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with PF00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Lin, C, Zou, X.F, Zhang, J, Li, J.
Deposit date:2023-04-16
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with PF00835231
To Be Published
8WZQ
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Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with CCF0058981
Descriptor: 2-(benzotriazol-1-yl)-~{N}-[(3-chlorophenyl)methyl]-~{N}-[4-(1~{H}-imidazol-5-yl)phenyl]ethanamide, 3C-like proteinase nsp5
Authors:Zou, X.F, Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
Deposit date:2023-11-02
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Crystal structure of SARS-CoV-2 main protease (M pro ) mutants in complex with the non-covalent inhibitor CCF0058981.
Biochem.Biophys.Res.Commun., 692, 2024
8J37
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Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with PF00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Lin, C, Zou, X.F, Zhang, J, Li, J.
Deposit date:2023-04-16
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with PF00835231
To Be Published
8J38
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Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with PF00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Lin, C, Zou, X.F, Zhang, J, Li, J.
Deposit date:2023-04-16
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.72 Å)
Cite:Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with PF00835231
To Be Published
8TV6
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SARS-CoV-2 Mac1 in complex with MDOLL-0169
Descriptor: (1R,6R)-6-{[3-(methoxycarbonyl)-5,6,7,8-tetrahydro-4H-cyclohepta[b]thiophen-2-yl]carbamoyl}cyclohex-3-ene-1-carboxylic acid, DI(HYDROXYETHYL)ETHER, GLYCEROL, ...
Authors:Wazir, S, Maksimainen, M, Lehtio, L.
Deposit date:2023-08-17
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Discovery of 2-amide-3-methylester thiophenes inhibiting SARS-CoV-2 ADP-ribosyl hydrolysing macrodomain and coronavirus replication
To Be Published
8WZP
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Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with CCF0058981
Descriptor: 2-(benzotriazol-1-yl)-~{N}-[(3-chlorophenyl)methyl]-~{N}-[4-(1~{H}-imidazol-5-yl)phenyl]ethanamide, 3C-like proteinase nsp5
Authors:Jiang, H.H, Zou, X.F, Zhou, X.L, Zhang, J, Li, J.
Deposit date:2023-11-02
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.76 Å)
Cite:Crystal structure of SARS-CoV-2 main protease (M pro ) mutants in complex with the non-covalent inhibitor CCF0058981.
Biochem.Biophys.Res.Commun., 692, 2024
8J35
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Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with PF00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Lin, C, Zou, X.F, Zhang, J, Li, J.
Deposit date:2023-04-16
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with PF00835231
To Be Published
9EPL
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Mpro from SARS-CoV-2 with 298Q mutation
Descriptor: 1,2-ETHANEDIOL, GLYCEROL, Non-structural protein 11, ...
Authors:Plewka, J, Lis, K, Czarna, A, Pyrc, K, Kantyka, T, Chykunova, Y.
Deposit date:2024-03-18
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 M pro oligomerization as a potential target for therapy.
Int.J.Biol.Macromol., 2024
8J3A
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Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with PF00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Lin, C, Zou, X.F, Zhang, J, Li, J.
Deposit date:2023-04-16
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with PF00835231
To Be Published
9EPM
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Mpro from SARS-CoV-2 with 4A mutation
Descriptor: Non-structural protein 11
Authors:Plewka, J, Lis, K, Czarna, A, Pyrc, K, Kantyka, T, Chykunova, Y.
Deposit date:2024-03-19
Release date:2024-04-17
Method:X-RAY DIFFRACTION (1.981 Å)
Cite:SARS-CoV-2 M pro oligomerization as a potential target for therapy.
Int.J.Biol.Macromol., 2024
8J32
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Crystal structure of SARS-Cov-2 main protease in complex with PF00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Lin, C, Zou, X.F, Zhang, J, Li, J.
Deposit date:2023-04-16
Release date:2024-04-17
Method:X-RAY DIFFRACTION (2.21 Å)
Cite:Crystal structure of SARS-Cov-2 main protease in complex with PF00835231
To Be Published
8KHC
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SARS-CoV-2 Omicron spike in complex with 5817 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 5817 Fab, ...
Authors:Cao, L, Wang, X.
Deposit date:2023-08-21
Release date:2024-04-17
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Identification of a broad sarbecovirus neutralizing antibody targeting a conserved epitope on the receptor-binding domain.
Cell Rep, 43, 2024
8KHD
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The interface structure of Omicron RBD binding to 5817 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 5817, Light chain of 5817, ...
Authors:Cao, L, Wang, X.
Deposit date:2023-08-21
Release date:2024-04-17
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Identification of a broad sarbecovirus neutralizing antibody targeting a conserved epitope on the receptor-binding domain.
Cell Rep, 43, 2024
8F2X
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Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, WRAIR-2123 Fab Heavy chain, ...
Authors:Sankhala, R.S, Joyce, G.M.
Deposit date:2022-11-08
Release date:2024-04-17
Method:X-RAY DIFFRACTION (3.501 Å)
Cite:Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain
To Be Published

218500

PDB entries from 2024-04-17

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