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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)
8GFU
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Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304, in complex with nirmatrelvir (NMV)
Descriptor: 3C-like proteinase nsp5, Nirmatrelvir
Authors:Kovalevsky, A, Coates, L.
Deposit date:2023-03-08
Release date:2023-07-12
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.
J.Biol.Chem., 299, 2023
8GQC
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Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.35 angstrom resolution)
Descriptor: Papain-like protease nsp3
Authors:Qin, B, Li, Z, Aumonier, S, Wang, M, Cui, S.
Deposit date:2022-08-30
Release date:2023-07-12
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:Identification of the SARS-unique domain of SARS-CoV-2 as an antiviral target.
Nat Commun, 14, 2023
8GTO
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cryo-EM structure of Omicron BA.5 S protein in complex with XGv282
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:Xia, X.Y, Zhang, Y.Y, Chi, X.M, Huang, B.D, Wu, L.S, Zhou, Q.
Deposit date:2022-09-08
Release date:2023-07-12
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants.
Cell Discov, 9, 2023
8GTP
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cryo-EM structure of Omicron BA.5 S protein in complex with XGv289
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:Xia, X.Y, Zhang, Y.Y, Chi, X.M, Huang, B.D, Wu, L.S, Zhou, Q.
Deposit date:2022-09-08
Release date:2023-07-12
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants.
Cell Discov, 9, 2023
8GTQ
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cryo-EM structure of Omicron BA.5 S protein in complex with S2L20
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Xia, X.Y, Zhang, Y.Y, Chi, X.M, Huang, B.D, Wu, L.S, Zhou, Q.
Deposit date:2022-09-08
Release date:2023-07-12
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants.
Cell Discov, 9, 2023
8HBL
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Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.58 angstrom resolution)
Descriptor: GLYCEROL, LITHIUM ION, Non-structural protein 3, ...
Authors:Qin, B, Li, Z, Aumonier, S, Wang, M, Cui, S.
Deposit date:2022-10-29
Release date:2023-07-12
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Identification of the SARS-unique domain of SARS-CoV-2 as an antiviral target.
Nat Commun, 14, 2023
7Y6K
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Cryo-EM structure of SARS-CoV-2 receptor binding domain in complex with K202.B bispecific antibody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab region of heavy chain from K202.B, bispecific antibody, ...
Authors:Yoo, Y, Cho, H.S.
Deposit date:2022-06-20
Release date:2023-07-19
Method:ELECTRON MICROSCOPY (3.34 Å)
Cite:Cryo-EM structure of SARS-CoV-2 receptor binding domain in complex with K202.B bispecific antibody
To Be Published
7YBG
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Crystal structure of the SARS-CoV-2 papain-like protease (C111S mutant)
Descriptor: 2,3-DIHYDROXY-1,4-DITHIOBUTANE, CHLORIDE ION, MALONIC ACID, ...
Authors:Zeng, R, Lei, J.
Deposit date:2022-06-29
Release date:2023-07-19
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of the SARS-CoV-2 papain-like protease (C111S mutant)
To Be Published
7YH6
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Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, NIV-8 Fab light chain, ...
Authors:Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-07-12
Release date:2023-07-19
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
7YH7
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SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, ...
Authors:Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y.
Deposit date:2022-07-13
Release date:2023-07-19
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
7YHW
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Cryo-EM structure of SARS-CoV-2 Omicron BA.2.12.1 RBD in complex with human ACE2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2022-07-14
Release date:2023-07-19
Last modified:2023-08-02
Method:ELECTRON MICROSCOPY (3.09 Å)
Cite:Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Nat Commun, 14, 2023
7YJ3
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BU of 7yj3 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with human ACE2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2022-07-19
Release date:2023-07-19
Last modified:2023-08-02
Method:ELECTRON MICROSCOPY (3.14 Å)
Cite:Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Nat Commun, 14, 2023
7YV8
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Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with golden hamster ACE2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike glycoprotein, ...
Authors:Zhao, Z.N, Xie, Y.F, Chai, Y, Qi, J.X, Gao, G.F.
Deposit date:2022-08-18
Release date:2023-07-19
Last modified:2023-08-02
Method:ELECTRON MICROSCOPY (2.94 Å)
Cite:Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Nat Commun, 14, 2023
7YVU
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Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Zhao, Z.N, Xie, Y.F, Chai, Y, Qi, J.X, Gao, G.F.
Deposit date:2022-08-19
Release date:2023-07-19
Last modified:2023-08-02
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Nat Commun, 14, 2023
8DNT
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BU of 8dnt by Molmil
SARS-CoV-2 specific T cell receptor
Descriptor: Beta-2-microglobulin, MHC class I antigen alpha chain, Nucleoprotein, ...
Authors:Gallagher, D.T, Wu, D, Gowthaman, R, Pierce, B.G, Mariuzza, R.A, Weng, N.P.
Deposit date:2022-07-11
Release date:2023-07-19
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.18 Å)
Cite:SARS-CoV-2 infection establishes a stable and age-independent CD8 + T cell response against a dominant nucleocapsid epitope using restricted T cell receptors.
Nat Commun, 14, 2023
8EL2
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SARS-CoV-2 RBD bound to neutralizing antibody Fab ICO-hu23
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab ICO-hu23 Heavy Chain, Fab ICO-hu23 Light Chain, ...
Authors:Besaw, J.E, Kuo, A, Morizumi, T, Ernst, O.P.
Deposit date:2022-09-22
Release date:2023-07-19
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.89 Å)
Cite:Broadly neutralizing humanized SARS-CoV-2 antibody binds to a conserved epitope on Spike and provides antiviral protection through inhalation-based delivery in non-human primates.
Plos Pathog., 19, 2023
8ELJ
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SARS-CoV-2 spike glycoprotein in complex with the ICO-hu23 neutralizing antibody Fab fragment
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ICO-hu23 antibody Fab heavy chain, ...
Authors:Yee, A.W, Morizumi, T, Kim, K, Kuo, A, Ernst, O.P.
Deposit date:2022-09-24
Release date:2023-07-19
Last modified:2023-08-16
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Broadly neutralizing humanized SARS-CoV-2 antibody binds to a conserved epitope on Spike and provides antiviral protection through inhalation-based delivery in non-human primates.
Plos Pathog., 19, 2023
8GRY
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BU of 8gry by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with rat ACE2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Zhao, Z.N, Xie, Y.F, Chai, Y, Qi, J.X, Gao, G.F.
Deposit date:2022-09-03
Release date:2023-07-19
Last modified:2023-08-02
Method:ELECTRON MICROSCOPY (3.29 Å)
Cite:Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Nat Commun, 14, 2023
8H06
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Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with human ACE2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2022-09-28
Release date:2023-07-19
Last modified:2023-08-02
Method:ELECTRON MICROSCOPY (2.66 Å)
Cite:Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Nat Commun, 14, 2023
8H5C
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Structure of SARS-CoV-2 Omicron BA.2.75 RBD in complex with human ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Zhao, Z.N, Bai, B, Liu, K.F, Qi, J.X, Gao, G.F.
Deposit date:2022-10-12
Release date:2023-07-19
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Nat Commun, 14, 2023
7UR9
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BU of 7ur9 by Molmil
SARS-Cov2 Main protease in complex with inhibitor CDD-1845
Descriptor: (2P)-2-(isoquinolin-4-yl)-1-[4-(methylamino)-4-oxobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide, 3C-like proteinase nsp5
Authors:Lu, S, Palzkill, T.
Deposit date:2022-04-21
Release date:2023-07-26
Last modified:2023-08-16
Method:X-RAY DIFFRACTION (2.16 Å)
Cite:DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors.
Commun Chem, 6, 2023
7URB
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Sars-Cov2 Main Protease in complex with CDD-1733
Descriptor: (2P)-2-(isoquinolin-4-yl)-1-[(1s,3R)-3-(methylcarbamoyl)cyclobutyl]-N-{(1S)-1-[4-(trifluoromethyl)phenyl]butyl}-1H-benzimidazole-7-carboxamide, 3C-like proteinase
Authors:Lu, S, Palzkill, T, Matzuk, M.M, Judge, A.
Deposit date:2022-04-21
Release date:2023-07-26
Last modified:2023-08-16
Method:X-RAY DIFFRACTION (2.14 Å)
Cite:DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors.
Commun Chem, 6, 2023
7US4
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Sars-Cov2 Main Protease in complex with CDD-1819
Descriptor: (2P)-2-(isoquinolin-4-yl)-1-[(1s,3R)-3-(methylcarbamoyl)cyclobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide, 3C-like proteinase
Authors:Lu, S, Palzkill, T, Matzuk, M.M, Judge, A.
Deposit date:2022-04-22
Release date:2023-07-26
Last modified:2023-08-16
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors.
Commun Chem, 6, 2023
8CMB
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Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S486-505
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-ETHANETHIOL, HLA class II histocompatibility antigen, ...
Authors:MacLachlan, B.J, Mason, G.H, Godkin, A.J, Rizkallah, P.J.
Deposit date:2023-02-19
Release date:2023-07-26
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Cell Rep, 42, 2023
8CMC
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Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
Descriptor: 1,2-ETHANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, HLA class II histocompatibility antigen, ...
Authors:MacLachlan, B.J, Mason, G.H, Sourfield, D.O, Godkin, A.J, Rizkallah, P.J.
Deposit date:2023-02-19
Release date:2023-07-26
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (1.42 Å)
Cite:Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity.
Cell Rep, 42, 2023

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