COVID-19 featured content

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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)

All entries (4406)Repr. entries (1944)Latest entries (19)

7SGU

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder608 inhibitor
Descriptor:	5-amino-N-(naphthalen-1-yl)pyridine-3-carboxamide, CHLORIDE ION, FORMIC ACID, ...
Authors:	Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2021-10-07
Release date:	2021-10-20
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.79 Å)
Cite:	Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder608 inhibitor To Be Published

7SGV

Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor
Descriptor:	CHLORIDE ION, N-(naphthalen-1-yl)pyridine-3-carboxamide, Papain-like protease, ...
Authors:	Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2021-10-07
Release date:	2021-10-20
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor To Be Published

7SGW

Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor
Descriptor:	CHLORIDE ION, N-(naphthalen-1-yl)pyridine-3-carboxamide, Non-structural protein 3, ...
Authors:	Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2021-10-07
Release date:	2021-10-20
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.95 Å)
Cite:	Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor To Be Published

7SI9

Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with PF-07321332
Descriptor:	(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase
Authors:	Kovalevsky, A, Kneller, D.W, Coates, L.
Deposit date:	2021-10-12
Release date:	2021-10-20
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease Nat Commun, 13, 2022

7V26

XG005-bound SARS-CoV-2 S
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, XG005 Heavy chain, ...
Authors:	Zhan, W.Q, Zhang, X, Sun, L, Chen, Z.G.
Deposit date:	2021-08-07
Release date:	2021-10-20
Last modified:	2022-07-06
Method:	ELECTRON MICROSCOPY (3.85 Å)
Cite:	An ultrapotent pan-beta-coronavirus lineage B ( beta-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope. Protein Cell, 13, 2022

7V2A

SARS-CoV-2 Spike trimer in complex with XG014 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, The heavy chain of XG014, ...
Authors:	Wang, K, Wang, X, Pan, L.
Deposit date:	2021-08-07
Release date:	2021-10-20
Last modified:	2022-07-06
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	An ultrapotent pan-beta-coronavirus lineage B ( beta-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope. Protein Cell, 13, 2022

7N3K

Oridonin-bound SARS-CoV-2 Nsp9
Descriptor:	(1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one, Non-structural protein 9, SULFATE ION
Authors:	Littler, D.R, Gully, B.S, Rossjohn, J.
Deposit date:	2021-06-01
Release date:	2021-10-27
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein. J.Biol.Chem., 297, 2021

7S3N

SARS-CoV-2 S stem helix peptide bound to Fab22
Descriptor:	Fab22 Heavy Chain, Fab22 Light Chain, Spike glycoprotein
Authors:	Goldsmith, J.A, McLellan, J.S.
Deposit date:	2021-09-07
Release date:	2021-10-27
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Stabilized coronavirus spike stem elicits a broadly protective antibody. Cell Rep, 37, 2021

7VNU

Crystal structure of the N-terminal domain of SARS-CoV-2 nucleocapsid protein
Descriptor:	ACETATE ION, Nucleoprotein
Authors:	Zhou, R.J, Ni, X.C, Lei, J.
Deposit date:	2021-10-12
Release date:	2021-10-27
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.95 Å)
Cite:	Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2. Commun Biol, 6, 2023

7DAT

The crystal structure of COVID-19 main protease treated by AF
Descriptor:	COVID-19 MAIN PROTEASE, GOLD ION
Authors:	He, Z.S, He, B, Cao, P, Jiang, H.D, Gong, Y, Gao, X.Y.
Deposit date:	2020-10-18
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.75 Å)
Cite:	A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster. Nano Today, 44, 2022

7DAU

The crystal structure of COVID-19 main protease treated by GA
Descriptor:	COVID-19 MAIN PROTEASE, GOLD ION
Authors:	He, Z.S, He, B, Cao, P, Jiang, H.D, Gong, Y, Gao, X.Y.
Deposit date:	2020-10-18
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.72 Å)
Cite:	A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster. Nano Today, 44, 2022

7DAV

The native crystal structure of COVID-19 main protease
Descriptor:	COVID-19 MAIN PROTEASE
Authors:	He, Z.S, He, B, Cao, P, Jiang, H.D, Gong, Y, Gao, X.Y.
Deposit date:	2020-10-18
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.77 Å)
Cite:	A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster. Nano Today, 44, 2022

7EKC

Structure of SARS-CoV-2 Gamma variant spike receptor-binding domain complexed 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, Angiotensin-converting enzyme 2, ...
Authors:	Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:	2021-04-05
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.8 Å)
Cite:	Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun, 12, 2021

7EKE

Structure of SARS-CoV-2 spike receptor-binding domain F486L mutation complexed with human ACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:	Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:	2021-04-05
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.7 Å)
Cite:	Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun, 12, 2021

7EKF

Structure of SARS-CoV-2 Alpha variant spike receptor-binding domain complexed 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, Angiotensin-converting enzyme 2, ...
Authors:	Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:	2021-04-05
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.85 Å)
Cite:	Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun, 12, 2021

7EKG

Structure of SARS-CoV-2 Beta variant spike receptor-binding domain complexed 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, Angiotensin-converting enzyme 2, ...
Authors:	Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:	2021-04-05
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.63 Å)
Cite:	Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun, 12, 2021

7EKH

Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with human ACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:	Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:	2021-04-05
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.4 Å)
Cite:	Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun, 12, 2021

7N5H

Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion SARS-CoV-2 spike glycoprotein
Descriptor:	2-36 Fab heavy chain, 2-36 Fab light chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Casner, R.G, Cerutti, G, Shapiro, L.
Deposit date:	2021-06-05
Release date:	2021-11-03
Last modified:	2022-11-16
Method:	ELECTRON MICROSCOPY (3.24 Å)
Cite:	A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerg Microbes Infect, 11, 2022

7SBK

Closed state of pre-fusion SARS-CoV-2 Delta variant spike 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:	2021-09-25
Release date:	2021-11-03
Last modified:	2021-12-22
Method:	ELECTRON MICROSCOPY (3.44 Å)
Cite:	Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science, 374, 2021

7SBO

One RBD-up 2 of pre-fusion SARS-CoV-2 Delta variant spike 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:	2021-09-25
Release date:	2021-11-03
Last modified:	2021-12-22
Method:	ELECTRON MICROSCOPY (3.44 Å)
Cite:	Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science, 374, 2021

7SBP

Closed state of pre-fusion SARS-CoV-2 Kappa variant spike 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:	2021-09-25
Release date:	2021-11-03
Last modified:	2021-12-22
Method:	ELECTRON MICROSCOPY (3.44 Å)
Cite:	Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science, 374, 2021

7SBQ

One RBD-up 1 of pre-fusion SARS-CoV-2 Kappa variant spike 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:	2021-09-25
Release date:	2021-11-03
Last modified:	2021-12-22
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science, 374, 2021

7SBR

One RBD-up 2 of pre-fusion SARS-CoV-2 Kappa variant spike 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:	2021-09-25
Release date:	2021-11-03
Last modified:	2021-12-22
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science, 374, 2021

7SBS

One RBD-up 1 of pre-fusion SARS-CoV-2 Gamma variant spike 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:	2021-09-25
Release date:	2021-11-03
Last modified:	2021-12-22
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science, 374, 2021

7VH8

Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332
Descriptor:	(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase, DIMETHYL SULFOXIDE
Authors:	Zhao, Y, Zhang, Q, Yang, H, Rao, Z.
Deposit date:	2021-09-21
Release date:	2021-11-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.59 Å)
Cite:	Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332. Protein Cell, 13, 2022

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Total results:	4406
Displayed results:	25
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