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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
9UHT
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BU of 9uht by Molmil
SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP
Descriptor: Helicase nsp13, Non-structural protein 7, Non-structural protein 8, ...
Authors:Huang, Y.C, Liu, Y.X, Lou, Z.Y, Rao, Z.H, Yan, L.M.
Deposit date:2025-04-14
Release date:2025-06-11
Method:ELECTRON MICROSCOPY (2.89 Å)
Cite:Response to Matter Arising: Substrate selection and transition state support the mechanism for GTP-mediate RNA capping catalyzed by SARS-CoV-2 NiRAN
To Be Published
9C7X
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BU of 9c7x by Molmil
Crystal structure of SARS-CoV-2 antibody 1H06 in complex with a HR2 peptide
Descriptor: Heavy Chain of SARS-CoV-2 antibody 1H06, Light Chain of SARS-CoV-2 antibody 1H06, Spike protein S2'
Authors:Van Wazer, D.J, Zhou, T, Kwong, P.D.
Deposit date:2024-06-11
Release date:2025-06-18
Method:X-RAY DIFFRACTION (1.96 Å)
Cite:SARS-CoV-2 Peptide Immunization in Mice Elicits Broadly Neutralizing Antibodies Targeting Cryptic S2 Helical-Stem Epitope
To Be Published
9EEI
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BU of 9eei by Molmil
Crystal structure of the SARS-CoV-2 Omicron nsp5 main protease (Mpro) E166V mutant in complex with inhibitor GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Neilsen, G, Kirby, K.A, Sarafianos, S.G.
Deposit date:2024-11-19
Release date:2025-06-18
Method:X-RAY DIFFRACTION (2.76 Å)
Cite:Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.
Sci Adv, 11, 2025
9EET
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BU of 9eet by Molmil
Crystal structure of the SARS-CoV-2 nsp5 main protease (Mpro) E166V mutant in complex with inhibitor GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Neilsen, G, Kirby, K.A, Sarafianos, S.G.
Deposit date:2024-11-19
Release date:2025-06-18
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.
Sci Adv, 11, 2025
9EEV
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BU of 9eev by Molmil
Crystal structure of the SARS-CoV-2 Omicron nsp5 main protease (Mpro) E166V mutant in complex with inhibitor Nirmatrelvir (PF-07321332)
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-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
Authors:Neilsen, G, Kirby, K.A, Sarafianos, S.G.
Deposit date:2024-11-19
Release date:2025-06-18
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.
Sci Adv, 11, 2025
9FMW
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BU of 9fmw by Molmil
Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6
Descriptor: Fab of neutralizing mAb K501SP6 heavy chain, Fab of neutralizing mAb K501SP6 light chain, Spike glycoprotein,Fibritin
Authors:Bjoernsson, K.H, Walker, M.R, Raghavan, S.S.R, Ward, A.B, Barfod, L.K.
Deposit date:2024-06-07
Release date:2025-06-18
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6
To Be Published
9IKZ
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BU of 9ikz by Molmil
SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3-
Descriptor: BERYLLIUM TRIFLUORIDE ION, GUANOSINE-5'-DIPHOSPHATE, Helicase nsp13, ...
Authors:Yan, L.M, Huang, Y.C, Liu, Y.X, Rao, Z.H, Lou, Z.Y.
Deposit date:2024-06-29
Release date:2025-06-18
Method:ELECTRON MICROSCOPY (3.14 Å)
Cite:Substrate selection and transition reveal the mechanism for RNA capping catalyzed by SARS-CoV-2 NiRAN
To Be Published
9VAO
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BU of 9vao by Molmil
Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2
Descriptor: GLYCEROL, PHOSPHATE ION, Papain-like protease nsp3, ...
Authors:Arya, R, Ganesh, J, Prashar, V, Kumar, M.
Deposit date:2025-06-03
Release date:2025-06-18
Method:X-RAY DIFFRACTION (1.82 Å)
Cite:Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2
To Be Published
9CPP
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BU of 9cpp by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-17 and CC12.3
Descriptor: CC12.3 Fab heavy chain, CC12.3 Fab light chain, CITRIC ACID, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.19 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPQ
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BU of 9cpq by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-44 and CC12.3
Descriptor: CC12.3 Fab heavy chain, CC12.3 Fab light chain, CITRIC ACID, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.88 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPR
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BU of 9cpr by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-90 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPS
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BU of 9cps by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-91 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.03 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPT
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BU of 9cpt by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-92 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.51 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPU
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BU of 9cpu by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0304 and CC12.3
Descriptor: C03-0304 Fab heavy chain, C03-0304 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPV
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BU of 9cpv by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0614 and CC12.3
Descriptor: C03-0614 Fab heavy chain, C03-0614 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPW
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BU of 9cpw by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-1036 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C11-1036 Fab heavy chain, C11-1036 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPX
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BU of 9cpx by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0138 and CC12.3
Descriptor: C03-0138 Fab heavy chain, C03-0138 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPY
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BU of 9cpy by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-0860 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, C11-0860 Fab heavy chain, C11-0860 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9P0F
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BU of 9p0f by Molmil
Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
Descriptor: Non-structural protein 4, SODIUM ION
Authors:Minasov, G, Shuvalova, L, Brunzelle, J.S, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:2025-06-06
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
To Be Published
9CFE
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BU of 9cfe by Molmil
Cryo-EM Local Refinement of Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFF
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BU of 9cff by Molmil
Cryo-EM Refinement of Antibody 19-77 in complex with SARS-CoV-2 HK.3 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFG
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BU of 9cfg by Molmil
Cryo-EM Refinement of Antibody 19-77 R71V in complex with SARS-CoV-2 HK.3 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFH
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BU of 9cfh by Molmil
Cryo-EM Refinement of Antibody 19-77 R71V in complex with SARS-CoV-2 JD.1.1 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9G0H
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BU of 9g0h by Molmil
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17A
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Yang, C.-C, Strater, N, Sylvester, K, Muller, C.E, Yang, M, Lee, M.K, Gao, S, Song, L, Liu, X, Kim, M, Zhan, P.
Deposit date:2024-07-08
Release date:2025-07-02
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Miniaturized Modular Click Chemistry-enabled Rapid Discovery of Unique SARS-CoV-2 M pro Inhibitors With Robust Potency and Drug-like Profile.
Adv Sci, 11, 2024
9G0I
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BU of 9g0i by Molmil
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17B
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, IMIDAZOLE, ...
Authors:Yang, C.-C, Strater, N, Sylvester, K, Muller, C.E, Yang, M, Lee, M.K, Gao, S, Song, L, Liu, X, Kim, M, Zhan, P.
Deposit date:2024-07-08
Release date:2025-07-02
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:Miniaturized Modular Click Chemistry-enabled Rapid Discovery of Unique SARS-CoV-2 M pro Inhibitors With Robust Potency and Drug-like Profile.
Adv Sci, 11, 2024

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