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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 (4459)Repr. entries (1984)Latest entries (16)
5SML
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PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework -- Crystal structure of SARS-CoV-2 main protease in complex with Z68337194 (Mpro-IBM0045)
Descriptor: 3C-like proteinase, 6-{[(3,4-dichlorophenyl)methyl](methyl)amino}pyridine-3-sulfonamide, DIMETHYL SULFOXIDE
Authors:Fearon, D, Owen, C.D, Lukacik, P, Strain-Damerell, C.M, von Delft, F.
Deposit date:2022-04-20
Release date:2023-04-26
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.53 Å)
Cite:PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework
To Be Published
5SMM
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PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework -- Crystal structure of SARS-CoV-2 main protease in complex with Z1633315555 (Mpro-IBM0058)
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, N-[4-(3-fluorophenyl)oxan-4-yl]-2-(3-hydroxyphenyl)acetamide
Authors:Fearon, D, Owen, C.D, Lukacik, P, Strain-Damerell, C.M, von Delft, F.
Deposit date:2022-04-20
Release date:2023-04-26
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework
To Be Published
5SMN
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PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework -- Crystal structure of SARS-CoV-2 main protease in complex with Z1365651030 (Mpro-IBM0078)
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, N-(1-cyanocyclopropyl)-1-(3-methylpyridin-4-yl)piperidine-4-carboxamide
Authors:Fearon, D, Owen, C.D, Lukacik, P, Strain-Damerell, C.M, von Delft, F.
Deposit date:2022-04-20
Release date:2023-04-26
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.36 Å)
Cite:PanDDA analysis group deposition of SARS-CoV-2 main protease ligands identified from single sequence-guideddeep generative framework
To Be Published
7UM2
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SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01
Descriptor: Beta-2-microglobulin, CADMIUM ION, HLA class I antigen, ...
Authors:Szeto, C, Gras, S.
Deposit date:2022-04-06
Release date:2023-04-26
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.63 Å)
Cite:SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01
To Be Published
7UR1
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SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01
Descriptor: Beta-2-microglobulin, HLA class I antigen, SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL)
Authors:Szeto, C, Ahn, Y.M, Gras, S.
Deposit date:2022-04-21
Release date:2023-04-26
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.17 Å)
Cite:SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01
To Be Published
7XIK
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SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex
Descriptor: B38 Fab heavy chain, B38 Fab light chain, Spike protein S1
Authors:Shi, R, Wang, Y, Wu, Z, Han, X, Yan, J.
Deposit date:2022-04-13
Release date:2023-04-26
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.89 Å)
Cite:SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex
To Be Published
7XIL
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SARS-CoV-2-Beta-RBD and B38-GWP/P-VK antibody complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, B38 Fab heavy chain, B38 Fab light chain, ...
Authors:Shi, R, Wang, Y, Wu, Z, Han, X, Yan, J.
Deposit date:2022-04-13
Release date:2023-04-26
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.91 Å)
Cite:SARS-CoV-2-Beta-RBD and B38-GWP/P-VK antibody complex
To Be Published
7XS8
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Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-1H1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, P5S-1H1 Heavy chain, P5S-1H1 Light chain, ...
Authors:Wang, X, Wang, Z.
Deposit date:2022-05-13
Release date:2023-04-26
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
8DJJ
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Khan, M.B, Lu, J, Young, H.S, Lemieux, M.J.
Deposit date:2022-06-30
Release date:2023-04-26
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.51 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8DKZ
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Khan, M.B, Lu, J, Young, H.S, Lemieux, M.J.
Deposit date:2022-07-06
Release date:2023-04-26
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (3 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8EIR
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SARS-CoV-2 polyprotein substrate regulates the stepwise Mpro cleavage reaction
Descriptor: 3C-like proteinase nsp5, nsp7-nsp10 of Replicase polyprotein 1a
Authors:Narwal, M, Edwards, T, Armache, J.P, Murakami, K.S.
Deposit date:2022-09-15
Release date:2023-04-26
Last modified:2024-06-19
Method:ELECTRON MICROSCOPY (2.49 Å)
Cite:SARS-CoV-2 polyprotein substrate regulates the stepwise M pro cleavage reaction.
J.Biol.Chem., 299, 2023
8EJ9
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-09-16
Release date:2023-04-26
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8EKE
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Cryo-EM structure of SARS CoV-2 Mpro WT protease
Descriptor: 3C-like proteinase nsp5
Authors:Narwal, M, Edwards, T, Armache, J.P, Murakami, K.S.
Deposit date:2022-09-20
Release date:2023-04-26
Last modified:2024-06-19
Method:ELECTRON MICROSCOPY (3.36 Å)
Cite:SARS-CoV-2 polyprotein substrate regulates the stepwise M pro cleavage reaction.
J.Biol.Chem., 299, 2023
8GB0
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SARS-CoV-2 Spike H655Y variant, One RBD Open
Descriptor: Spike glycoprotein
Authors:Egri, S.B, Shen, K, Luban, J.
Deposit date:2023-02-24
Release date:2023-04-26
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness.
Biorxiv, 2023
8HEB
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SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab in the class 1 conformation
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:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-11-08
Release date:2023-04-26
Method:ELECTRON MICROSCOPY (3.53 Å)
Cite:Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2.
Biochem.Biophys.Res.Commun., 660, 2023
8HEC
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SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab in the class 2 conformation
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:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-11-08
Release date:2023-04-26
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2.
Biochem.Biophys.Res.Commun., 660, 2023
8HED
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Local refinement of the SARS-CoV-2 Spike trimer in complex with RmAb 9H1 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, Spike protein S1, ...
Authors:Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
Deposit date:2022-11-08
Release date:2023-04-26
Method:ELECTRON MICROSCOPY (3.59 Å)
Cite:Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2.
Biochem.Biophys.Res.Commun., 660, 2023
8DI3
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-06-28
Release date:2023-05-03
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8DKH
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-07-05
Release date:2023-05-03
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8DKJ
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BU of 8dkj by Molmil
Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-07-05
Release date:2023-05-03
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.11 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8DKK
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-07-05
Release date:2023-05-03
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8DKL
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-07-05
Release date:2023-05-03
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8DMN
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-07-08
Release date:2023-05-03
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8EJ7
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Polymorphism in SARS-CoV-2 Nsp5 main protease reveals differences in cleavage of viral and host substrates
Descriptor: 3C-like proteinase nsp5
Authors:Lu, J, Khan, M.B, Young, H.S, Lemieux, M.J.
Deposit date:2022-09-16
Release date:2023-05-03
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals.
Acs Cent.Sci., 9, 2023
8F0G
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Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody Fab 1C3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody 1C3 Fab Heavy Chain, ...
Authors:Yu, X, Zyla, D, Hastie, K.M, Saphire, E.O.
Deposit date:2022-11-02
Release date:2023-05-03
Method:ELECTRON MICROSCOPY (3.35 Å)
Cite:Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.
Cell Rep, 42, 2023

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