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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 (4406)Repr. entries (1944)Latest entries (19)
8HQ7
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Cryo-EM structure of SARS-CoV-2 Omicron Prototype RBD in complex with fab L4.65 and L5.34
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, fab L4.65, ...
Authors:Gao, G.F, Liu, S.
Deposit date:2022-12-13
Release date:2023-12-20
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HQG
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Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with inhibitor YH-53
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Wang, J, Zhang, J, Li, J.
Deposit date:2022-12-13
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with inhibitor YH-53
To Be Published
8HQH
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Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with inhibitor YH-53
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zou, X.F, Zhang, J, Li, J.
Deposit date:2022-12-13
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with inhibitor YH-53
To Be Published
8HQI
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Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with inhibitor YH-53
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Li, W.W, Zhang, J, Li, J.
Deposit date:2022-12-13
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with inhibitor YH-53
To Be Published
8HQJ
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Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with inhibitor YH-53
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zhou, X.L, Zhang, J, Li, J.
Deposit date:2022-12-13
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with inhibitor YH-53
To Be Published
8HQT
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The complex structure of COPI cargo sorting module with SARS-CoV-2 Spike KxHxx sorting motif
Descriptor: Coatomer subunit beta', SARS-CoV-2 Spike KxHxx motif
Authors:Ma, W.F, Nan, Y.N, Yang, M.R, Li, Y.Q.
Deposit date:2022-12-14
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Tighter ER retention of SARS-CoV-2 Omicron spike caused by a constellation of folding disruptive mutations
To Be Published
8HRD
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Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, IMCAS74 Fab heavy chain, IMCAS74 Fab light chain, ...
Authors:Zhao, R.C, Wu, L.L, Han, P.
Deposit date:2022-12-15
Release date:2023-12-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.86 Å)
Cite:Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
8HRI
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SARS-CoV-2 Delta variant spike protein
Descriptor: Spike glycoprotein
Authors:Xu, J, Cheng, H, Liu, N, Wang, H.W.
Deposit date:2022-12-15
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure
To Be Published
8HRJ
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SARS-CoV-2 Delta variant spike protein
Descriptor: Spike glycoprotein
Authors:Xu, J, Cheng, H, Liu, N, Wang, H.W.
Deposit date:2022-12-15
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure
To Be Published
8HRK
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SARS-CoV-2 Delta S-RBD-ACE2 complex
Descriptor: Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Xu, J, Meng, F, Liu, N, Wang, H.W.
Deposit date:2022-12-15
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure
To Be Published
8HRL
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SARS-CoV-2 Delta S-RBD-ACE2
Descriptor: Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Xu, J, Meng, F, Liu, N, Wang, H.W.
Deposit date:2022-12-15
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure
To Be Published
8HSM
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CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67
Descriptor: Beta-2-microglobulin, Ig-like domain-containing protein, PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67
To Be Published
8HSO
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CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.2 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
Descriptor: Beta-2-microglobulin, Ig-like domain-containing protein, PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.2 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
To Be Published
8HSW
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CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.1 ANGSTROM
Descriptor: Beta-2-microglobulin, Ig-like domain-containing protein, THR-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.03 Å)
Cite:CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.1 ANGSTROM
To Be Published
8HT1
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CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.4 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
Descriptor: Beta-2-microglobulin, Ig-like domain-containing protein, THR-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.4 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
To Be Published
8HT9
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CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.2 ANGSTROM
Descriptor: Beta-2-microglobulin, GLU-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL, Ig-like domain-containing protein
Authors:Wang, S.Q, Zhang, N.Z.
Deposit date:2022-12-20
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.2 ANGSTROM
To Be Published
8Q7S
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BU of 8q7s by Molmil
Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01
Descriptor: 1,2-ETHANEDIOL, 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE, GLYCEROL, ...
Authors:Guttler, T, Aksu, M, Gorlich, D.
Deposit date:2023-08-16
Release date:2023-12-20
Last modified:2024-01-17
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q93
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Crystal structure of the SARS-COV-2 RBD with neutralizing-VHHs Re30H02 and Re21D01
Descriptor: Nanobody Re21D01, Nanobody Re30H02, Spike protein S1
Authors:Aksu, M, Guttler, T, Rymarenko, O, Gorlich, D.
Deposit date:2023-08-19
Release date:2023-12-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q94
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Crystal structure of The SARS-COV-2 BA.2.75 RBD with neutralizing-VHHs Re32D03 and Ma3B12
Descriptor: Nanobody Ma3B12, Nanobody Re32D03, Spike protein S1
Authors:Aksu, M, Guttler, T, Gorlich, D.
Deposit date:2023-08-19
Release date:2023-12-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8Q95
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Crystal structure of the SARS-CoV-2 BA.1 RBD with neutralizing-VHHs Ma16B06 and Ma3F05
Descriptor: Nanobody Ma16B06, Nanobody Ma3F05, Spike protein S1
Authors:Aksu, M, Rymarenko, O, Guttler, T, Gorlich, D.
Deposit date:2023-08-19
Release date:2023-12-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters.
Antiviral Res., 221, 2023
8UH9
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Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-272
Descriptor: (1R,2S,5S)-N-{(1S,2S)-1-(5-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5, DI(HYDROXYETHYL)ETHER
Authors:Bulut, H, Hayashi, H, Kuwata, N, Tsuji, K, Das, D, Tamamura, H, Mitsuya, H.
Deposit date:2023-10-07
Release date:2023-12-20
Method:X-RAY DIFFRACTION (2.067 Å)
Cite:TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir
To Be Published
8XAB
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Crystal structure of Ubl1 domain of nonstructural protein 3 of SARS-CoV-2
Descriptor: GLYCEROL, Papain-like protease nsp3
Authors:Li, Y, Ke, Z.
Deposit date:2023-12-03
Release date:2023-12-20
Method:X-RAY DIFFRACTION (1.49 Å)
Cite:N-terminus of SARS-CoV-2 Nsp3 Interrupts RNA-driven Phase Separation of N Protein by Displacing RNA
To Be Published
7Y3O
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BU of 7y3o by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody BIOLS56
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of BIOLS56, Light chain of BIOLS56, ...
Authors:Rao, X, Gao, F, Wu, Y, Gao, F.
Deposit date:2022-06-11
Release date:2023-12-27
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
8BZN
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SARS-CoV-2 non-structural protein 10 (nsp10) variant T102I
Descriptor: CHLORIDE ION, DIMETHYL SULFOXIDE, Replicase polyprotein 1ab, ...
Authors:Wang, H, Rizvi, S.R.A, Dong, D, Lou, J, Wang, Q, Sopipong, W, Najar, F, Agarwal, P.K, Kozielski, F, Haider, S.
Deposit date:2022-12-15
Release date:2023-12-27
Last modified:2024-01-10
Method:X-RAY DIFFRACTION (2.19 Å)
Cite:Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16.
Elife, 12, 2023
8HN4
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Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope QYIKWPWYI
Descriptor: Beta-2-microglobulin, MHC class I antigen, SARS-CoV-2 T-cell epitope QYIKWPWYI
Authors:Deng, S.S, Jin, T.C, Xu, Z.H.
Deposit date:2022-12-07
Release date:2023-12-27
Method:X-RAY DIFFRACTION (2.853 Å)
Cite:Immune escape at SARS- CoV-2 killer T cell epitope
To be published

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