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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)
9ML8
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Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-B1 heavy chain, M8b-B1 light chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML9
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Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab
Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-C9 heavy chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:X-RAY DIFFRACTION (2.59 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9MRW
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Functional Implications of Hexameric Dynamics in SARS-CoV-2 Nsp15
Descriptor: Uridylate-specific endoribonuclease nsp15
Authors:Ketawala, G.K, Sonowal, M, Schrag, L, Fromme, R, Botha, S, Fromme, P.
Deposit date:2025-01-08
Release date:2025-06-04
Method:X-RAY DIFFRACTION (3 Å)
Cite:Functional implications of hexameric dynamics in SARS-CoV-2 Nsp15.
Protein Sci., 34, 2025
9MRY
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Functional Implications of HexamericDynamics in SARS-CoV-2 Nsp15
Descriptor: Uridylate-specific endoribonuclease nsp15
Authors:Ketawala, G.K, Sonowal, M, Schrag, L, Fromme, R, Botha, S, Fromme, P.
Deposit date:2025-01-09
Release date:2025-06-04
Method:X-RAY DIFFRACTION (3 Å)
Cite:Functional implications of hexameric dynamics in SARS-CoV-2 Nsp15.
Protein Sci., 34, 2025
8XCH
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SARS-CoV-2 Replication-Transcription Complex has a dimer-of-dimeric architecture (ddRTC) in pre-capping initiation.
Descriptor: ADENOSINE-5'-DIPHOSPHATE, Helicase, MAGNESIUM ION, ...
Authors:Yan, L, Lou, Z.
Deposit date:2023-12-09
Release date:2025-06-11
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis for template-product RNA duplex unwinding by SARS-CoV-2 helicase
To Be Published
8ZPQ
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Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab
Descriptor: 70fab-H, 70fab-L, Spike protein S1
Authors:Wu, Y, Gao, F.
Deposit date:2024-05-31
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab
To Be Published
8ZQ8
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SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039
Descriptor: 3C-like proteinase nsp5, CG-1039
Authors:Chen, X, Hou, K, Tang, X.
Deposit date:2024-06-01
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039
To Be Published
8ZT9
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The Crystal structure of mol066 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor: 3C-like proteinase, 6-[(6-chloranyl-2-propan-2-yl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione, GLYCEROL
Authors:Yan, M, Zhang, H.
Deposit date:2024-06-06
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities.
Bioorg.Chem., 154, 2025
8ZUC
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The Crystal structure of mol080 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor: 3C-like proteinase, 6-[[6-chloranyl-2-(3-methylbutyl)indazol-5-yl]amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione
Authors:Yan, M, Zhang, H.
Deposit date:2024-06-08
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities.
Bioorg.Chem., 154, 2025
9FC2
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The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4.
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, ...
Authors:Casasnovas, J.M, Fernandez, L.A, Silva, K.
Deposit date:2024-05-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.21 Å)
Cite:Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants.
Mabs, 17, 2025
9GUB
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SARS-CoV-2 Mac1 in complex with MCD-628
Descriptor: (2~{S})-3-(1~{H}-indol-3-yl)-2-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-ylamino)propanoic acid, Papain-like protease nsp3
Authors:Duong, M, Paakkonen, J, Lehtio, L.
Deposit date:2024-09-19
Release date:2025-06-11
Last modified:2025-06-25
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Identification of a series of pyrrolo-pyrimidine-based SARS-CoV-2 Mac1 inhibitors that repress coronavirus replication.
Mbio, 16, 2025
9NPX
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SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosomal subunit (local refinement of the 40S body)
Descriptor: 18S ribosomal RNA, 40S ribosomal protein S11, 40S ribosomal protein S13, ...
Authors:Gen, R, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:2025-03-11
Release date:2025-06-11
Method:ELECTRON MICROSCOPY (2.1 Å)
Cite:SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals.
Cell Rep, 44, 2025
9C7X
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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
9IKZ
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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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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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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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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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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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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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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

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PDB entries from 2025-07-09

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