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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 (4418)Repr. entries (1953)Latest entries (11)
7ZB6
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant C44S at 2.12 A resolution
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
Authors:Paknia, E, Rabe von Pappenheim, F, Funk, L.-M, Tittmann, K, Chari, A.
Deposit date:2022-03-23
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design.
Nat Commun, 15, 2024
7ZB7
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant Y54F at 1.63 A resolution
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, GLYCEROL
Authors:Paknia, E, Rabe von Pappenheim, F, Funk, L.-M, Tittmann, K, Chari, A.
Deposit date:2022-03-23
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.63 Å)
Cite:Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design.
Nat Commun, 15, 2024
7ZB8
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) variant K61A at 2.48 A resolution
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
Authors:Paknia, E, Rabe von Pappenheim, F, Funk, L.-M, Tittmann, K, Chari, A.
Deposit date:2022-03-23
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.48 Å)
Cite:Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design.
Nat Commun, 15, 2024
7ZF3
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SARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs
Descriptor: EY6A heavy chain, EY6A light chain, GLYCEROL, ...
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.15 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZF5
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SARS-CoV-2 Omicron RBD in complex with Omi-12 and Beta-54 Fabs
Descriptor: Beta-54 heavy chain, Beta-54 light chain, Omi-12 heavy chain, ...
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (5.32 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZF7
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SARS-CoV-2 Omicron BA.2 RBD in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.46 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZF8
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SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab
Descriptor: COVOX-150 heavy chain, COVOX-150 light chain, Spike protein S1
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZFB
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SARS-CoV-2 Omicron RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody C1, Omi-18 heavy chain, ...
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.08 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZFC
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SARS-CoV-2 Beta RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs
Descriptor: Nanobody C1, Omi-18 heavy chain, Omi-18 light chain, ...
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.24 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZFD
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SARS-CoV-2 Omicron RBD in complex with Omi-25 Fab
Descriptor: Omi-25 heavy chain, Omi-25 light chain, Spike protein S1
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.39 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZFE
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SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1
Descriptor: Nanobody C1, Omi-32 heavy chain, Omi-32 light chain, ...
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-01
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.25 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZR7
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OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Omi-42 heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2022-05-03
Release date:2022-06-01
Last modified:2023-11-22
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZR9
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OMI-2 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Omi-2 Fab heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2022-05-03
Release date:2022-06-01
Last modified:2022-06-22
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7ZRC
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OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Omi-38 Fab Heavy Chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2022-05-04
Release date:2022-06-01
Last modified:2022-06-22
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7R4I
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The SARS-CoV-2 spike in complex with the 2.15 neutralizing nanobody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Camel-derived nanobody 2.15, ...
Authors:Casasnovas, J.M, Melero, R, Arranz, R, Fernandez, L.A.
Deposit date:2022-02-08
Release date:2022-06-08
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron.
Front Immunol, 13, 2022
7R4Q
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The SARS-CoV-2 spike in complex with the 1.29 neutralizing nanobody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Camel-derived nanobody 1.29, ...
Authors:Casasnovas, J.M, Melero, R, Arranz, R, Fernandez, L.A.
Deposit date:2022-02-09
Release date:2022-06-08
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron.
Front Immunol, 13, 2022
7R4R
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The SARS-CoV-2 spike in complex with the 1.10 neutralizing nanobody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Camel-derived nanobody 1.10, ...
Authors:Casasnovas, J.M, Melero, R, Arranz, R, Fernandez, L.A.
Deposit date:2022-02-09
Release date:2022-06-08
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron.
Front Immunol, 13, 2022
7SD4
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SARS-CoV-2 Nucleocapsid N-terminal domain (N-NTD) protein
Descriptor: Nucleoprotein
Authors:Sarkar, S, Runge, B, Russell, R.W, Calero, D, Zeinalilathori, S, Quinn, C.M, Lu, M, Calero, G, Gronenborn, A.M, Polenova, T.
Deposit date:2021-09-29
Release date:2022-06-08
Last modified:2024-05-15
Method:SOLID-STATE NMR
Cite:Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain.
J.Am.Chem.Soc., 144, 2022
7UHC
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SARS-CoV-2 spike in complex with AHB2-2GS-SB175
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Multivalent miniprotein inhibitor AHB2-2GS-SB175, ...
Authors:Park, Y.J, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:2022-03-26
Release date:2022-06-08
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice.
Sci Transl Med, 14, 2022
7W6U
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Structure of SARS-CoV-2 spike receptor-binding domain complexed with its receptor equine ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
Authors:Xu, Z.P, Liu, K.F, Han, P, Qi, J.X.
Deposit date:2021-12-02
Release date:2022-06-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.56 Å)
Cite:Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses
Nat Commun, 13, 2022
7WRI
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Cryo-EM structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with mouse ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein, ...
Authors:Han, P, Xie, Y, Qi, J.
Deposit date:2022-01-26
Release date:2022-06-08
Last modified:2022-12-21
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:Broader-species receptor binding and structural bases of Omicron SARS-CoV-2 to both mouse and palm-civet ACE2s.
Cell Discov, 8, 2022
7WSK
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Crystal structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with civet ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Huang, B, Han, P, Qi, J.
Deposit date:2022-01-29
Release date:2022-06-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Broader-species receptor binding and structural bases of Omicron SARS-CoV-2 to both mouse and palm-civet ACE2s.
Cell Discov, 8, 2022
7XBY
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The crystal structure of SARS-CoV-2 Omicron BA.1 variant RBD in complex with equine ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, BROMIDE ION, ...
Authors:Xu, Z.P, Liu, K.F, Han, P, Qi, J.X.
Deposit date:2022-03-22
Release date:2022-06-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses.
Nat Commun, 13, 2022
7ZF4
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SARS-CoV-2 Omicron RBD in complex with Omi-9 Fab and nanobody F2
Descriptor: Nanobody F2, Omi-9 heavy chain, Omi-9 light chain, ...
Authors:Zhou, D, Huo, J, Ren, J, Stuart, D.I.
Deposit date:2022-04-01
Release date:2022-06-08
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (4.18 Å)
Cite:Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Cell, 185, 2022
7F0X
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A SARS-CoV-2 neutralizing antibody
Descriptor: Antibody, Spike protein S1
Authors:Zhang, G, Li, X, Guo, Y, Wang, Y, Yuan, S.
Deposit date:2021-06-07
Release date:2022-06-15
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:A SARS-CoV-2 neutralizing antibody
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