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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)
7UAR
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BU of 7uar by Molmil
Structure of the SARS-CoV-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1717
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C1717 Fab Heavy Chain, ...
Authors:Barnes, C.O.
Deposit date:2022-03-13
Release date:2022-04-27
Last modified:2022-06-22
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins.
Immunity, 55, 2022
7X7N
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3D model of the 3-RBD up single trimeric spike protein of SARS-CoV2 in the presence of synthetic peptide SIH-5.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, Synthetic peptide SIH-5
Authors:Khatri, B, Pramanick, I, Malladi, S.K, Rajmani, R.S, Kumar, S, Ghosh, P, Sengupta, N, Rahisuddin, R, Kumaran, S, Ringe, R.P, Varadarajan, R, Dutta, S, Chatterjee, J.
Deposit date:2022-03-10
Release date:2022-04-27
Last modified:2022-11-16
Method:ELECTRON MICROSCOPY (4.47 Å)
Cite:A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein.
Nat.Chem.Biol., 18, 2022
7RBU
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BU of 7rbu by Molmil
SARS-CoV-2 Spike in complex with PVI.V6-14 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, PVI.V6-14 Fab heavy chain, ...
Authors:Altomare, C.G, Bajic, G.
Deposit date:2021-07-06
Release date:2022-05-04
Last modified:2022-07-06
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain.
Mbio, 13, 2022
7RBV
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BU of 7rbv by Molmil
SARS-CoV-2 Spike in complex with PVI.V6-14 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, PVI.V6-14 Fab heavy chain, ...
Authors:Altomare, C.G, Bajic, G.
Deposit date:2021-07-06
Release date:2022-05-04
Last modified:2022-07-06
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain.
Mbio, 13, 2022
7U2D
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BU of 7u2d by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADG20
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, ADG20 heavy chain, ADG20 light chain, ...
Authors:Zhu, X, Yuan, M, Wilson, I.A.
Deposit date:2022-02-23
Release date:2022-05-04
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.76 Å)
Cite:A broad and potent neutralization epitope in SARS-related coronaviruses.
Proc.Natl.Acad.Sci.USA, 119, 2022
7U2E
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BU of 7u2e by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADI-55688
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, ADI-55688 heavy chain, ADI-55688 light chain, ...
Authors:Yuan, M, Zhu, X, Wilson, I.A.
Deposit date:2022-02-23
Release date:2022-05-04
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:A broad and potent neutralization epitope in SARS-related coronaviruses.
Proc.Natl.Acad.Sci.USA, 119, 2022
7URQ
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BU of 7urq by Molmil
Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CITRIC ACID, COV11 Fab HEAVY CHAIN, ...
Authors:Tolbert, W.D, Pazgier, M.
Deposit date:2022-04-22
Release date:2022-05-04
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.
Front Immunol, 14, 2023
7URS
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BU of 7urs by Molmil
Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 2
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, COV11 Fab HEAVY CHAIN, ...
Authors:Tolbert, W.D, Pazgier, M.
Deposit date:2022-04-22
Release date:2022-05-04
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.
Front Immunol, 14, 2023
7WE7
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BU of 7we7 by Molmil
SARS-CoV-2 Omicron variant spike protein in complex with Fab 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, Heavy chain of Fab 282, ...
Authors:Wang, X, Wang, L.
Deposit date:2021-12-23
Release date:2022-05-04
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WE8
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BU of 7we8 by Molmil
SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv265
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Fab 265, ...
Authors:Wang, X, Wang, L.
Deposit date:2021-12-23
Release date:2022-05-04
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WE9
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BU of 7we9 by Molmil
SARS-CoV-2 Omicron variant spike protein in complex with Fab 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:Wang, X, Wang, L.
Deposit date:2021-12-23
Release date:2022-05-04
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WEA
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BU of 7wea by Molmil
SARS-CoV-2 Omicron variant spike protein in complex with two XGv347 binding to one close state RBD and one open state RBD
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:Wang, X, Wang, L.
Deposit date:2021-12-23
Release date:2022-05-04
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WEC
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BU of 7wec by Molmil
SARS-CoV-2 Omicron variant spike protein with three XGv347 Fabs binding to three closed state RBDs
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:Wang, X, Wang, L.
Deposit date:2021-12-23
Release date:2022-05-04
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WEF
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BU of 7wef by Molmil
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv289
Descriptor: Spike protein S1, The heavy chain of Fab XGv289, The light chain of Fab XGv289
Authors:Wang, X, Wang, L.
Deposit date:2021-12-23
Release date:2022-05-04
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7Z3Z
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BU of 7z3z by Molmil
Locked Wuhan SARS-CoV2 Prefusion Spike ectodomain with lipid bound
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, STEARIC ACID, ...
Authors:Duyvesteyn, H.M.E, Carrique, L, Ren, J, Stuart, D.I, Fry, E.E.
Deposit date:2022-03-03
Release date:2022-05-04
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer
bioRxiv, 2020
7S6I
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BU of 7s6i by Molmil
SARS-CoV-2-6P-Mut2 S protein
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:Ozorowski, G, Torres, J.L, Ward, A.B.
Deposit date:2021-09-14
Release date:2022-05-11
Last modified:2022-05-25
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7S6J
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J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut2 S protein (conformation 1)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, J08 fragment antigen binding heavy chain variable domain, ...
Authors:Ozorowski, G, Torres, J.L, Ward, A.B.
Deposit date:2021-09-14
Release date:2022-05-11
Last modified:2022-05-25
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7S6K
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J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut2 S protein (conformation 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, J08 fragment antigen binding heavy chain variable domain, ...
Authors:Ozorowski, G, Torres, J.L, Ward, A.B.
Deposit date:2021-09-14
Release date:2022-05-11
Last modified:2022-05-25
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7S6L
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BU of 7s6l by Molmil
J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (conformation 3)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, J08 fragment antigen binding heavy chain variable domain, ...
Authors:Ozorowski, G, Torres, J.L, Ward, A.B.
Deposit date:2021-09-14
Release date:2022-05-11
Last modified:2022-05-25
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7SBU
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BU of 7sbu by Molmil
Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a highly potent antibody J08 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, J08 Fab heavy chain, ...
Authors:Liu, H, Wilson, I.A.
Deposit date:2021-09-25
Release date:2022-05-11
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.53 Å)
Cite:Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7UV5
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BU of 7uv5 by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin
Descriptor: 1,2-ETHANEDIOL, Papain-like protease nsp3, Ubiquitin, ...
Authors:Osipiuk, J, Tesar, C, Endres, M, Lanham, B.T, Wydorski, P, Fushman, D, Joachimiak, L, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2022-04-29
Release date:2022-05-11
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.
Nat Commun, 14, 2023
7WHI
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BU of 7whi by Molmil
The state 2 complex structure of Omicron spike with Bn03 (2-up RBD, 4 nanobodies)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Bn03_nano1, Bn03_nano2, ...
Authors:Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
Deposit date:2021-12-30
Release date:2022-05-11
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody.
Cell, 185, 2022
7WHK
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BU of 7whk by Molmil
The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Bn03_nano1, Bn03_nano2, ...
Authors:Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
Deposit date:2021-12-30
Release date:2022-05-11
Method:ELECTRON MICROSCOPY (3.01 Å)
Cite:Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody.
Cell, 185, 2022
7X9E
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Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 spike peptide
Descriptor: 76E1 Fab Heavy Chain, 76E1 Fab Light Chain, Spike peptide
Authors:Chen, X, Zhang, T, Ding, J, Sun, X, Sun, B.
Deposit date:2022-03-15
Release date:2022-05-11
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2.
Nat Microbiol, 7, 2022
7EPX
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BU of 7epx by Molmil
S protein of SARS-CoV-2 in complex with GW01
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:Shen, Y.P, Zhang, Y.Y, Yan, R.H, Li, Y.N, Zhou, Q.
Deposit date:2021-04-28
Release date:2022-05-18
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Novel sarbecovirus bispecific neutralizing antibodies with exceptional breadth and potency against currently circulating SARS-CoV-2 variants and sarbecoviruses.
Cell Discov, 8, 2022

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