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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 (5197)Repr. entries (2266)Latest entries (44)
9F7A
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BU of 9f7a by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R
Descriptor: Nucleoprotein, ZINC ION
Authors:Dhamotharan, K, Schlundt, A.
Deposit date:2024-05-03
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F7C
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BU of 9f7c by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I
Descriptor: Nucleoprotein, ZINC ION
Authors:Dhamotharan, K, Schlundt, A.
Deposit date:2024-05-03
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F83
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BU of 9f83 by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant D63G
Descriptor: Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A, Guenther, S.
Deposit date:2024-05-06
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9FBG
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BU of 9fbg by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P151S
Descriptor: Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A.
Deposit date:2024-05-13
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (2.54 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9GWO
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BU of 9gwo by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571126
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
Deposit date:2024-09-27
Release date:2024-11-20
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8RJ7
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BU of 8rj7 by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Camel-derived nanobody 1.29, LYSINE, ...
Authors:Casasnovas, J.M, Fernandez, L.A, Silva, K.
Deposit date:2023-12-20
Release date:2024-11-27
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
To Be Published
8YKJ
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BU of 8ykj by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with X77
Descriptor: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide, Non-structural protein 11
Authors:Zhou, X.L, Lin, C, Li, W.W, Zhang, J, Li, J.
Deposit date:2024-03-05
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKM
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BU of 8ykm by Molmil
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with X77
Descriptor: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
Authors:Zeng, P, Zhang, J, Li, J.
Deposit date:2024-03-05
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKN
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BU of 8ykn by Molmil
Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with X77
Descriptor: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide, Non-structural protein 11
Authors:Wang, J, Zhang, J, Li, J.
Deposit date:2024-03-05
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKO
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BU of 8yko by Molmil
Crystal structure of SARS-Cov-2 main protease P132H mutant in complex withX77
Descriptor: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
Authors:Li, W.W, Zhang, J, Li, J.
Deposit date:2024-03-05
Release date:2024-11-27
Method:X-RAY DIFFRACTION (2.11 Å)
Cite:Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKP
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BU of 8ykp by Molmil
Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with X77
Descriptor: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
Authors:Zou, X.F, Zhang, J, Li, J.
Deposit date:2024-03-05
Release date:2024-11-27
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKQ
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BU of 8ykq by Molmil
Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with X77
Descriptor: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
Authors:Zou, X.F, Zhang, J, Li, J.
Deposit date:2024-03-05
Release date:2024-11-27
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
9CRC
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Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 3 closed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Ke, Z, Croll, T.I, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRD
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BU of 9crd by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 1 open 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Ke, Z, Croll, T.I, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRE
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BU of 9cre by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 3 closed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Ke, Z, Croll, T.I, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRF
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BU of 9crf by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 1 open 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Ke, Z, Croll, T.I, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRG
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Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Gamma (P.1) variant 3 closed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Ke, Z, Kotecha, A, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRH
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BU of 9crh by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Delta (B.1.617.2) variant 3 closed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Ke, Z, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRI
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BU of 9cri by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Mu (B.1.621) variant 3 closed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Ke, Z, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9HBQ
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BU of 9hbq by Molmil
SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-indane-1-carboxamide
Descriptor: (1~{R})-~{N}-(3-chlorophenyl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Hanoulle, X, Charton, J, Deprez, B.
Deposit date:2024-11-08
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.795 Å)
Cite:SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-indane-1-carboxamide
To Be Published
9HC1
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BU of 9hc1 by Molmil
SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-N-[4-(2-oxopyrrolidin-1-yl)phenyl]indane-1-carboxamide
Descriptor: (1~{R})-~{N}-(3-chlorophenyl)-3-oxidanylidene-~{N}-[4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]-1,2-dihydroindene-1-carboxamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Hanoulle, X, Charton, J, Deprez, B.
Deposit date:2024-11-08
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.493 Å)
Cite:SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-N-[4-(2-oxopyrrolidin-1-yl)phenyl]indane-1-carboxamide
To Be Published
9HD8
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BU of 9hd8 by Molmil
SARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide
Descriptor: (1~{R})-~{N}-[4-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]phenyl]-~{N}-(3-chlorophenyl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide, 3C-like proteinase nsp5, SODIUM ION
Authors:Hanoulle, X, Charton, J, Deprez, B.
Deposit date:2024-11-12
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.696 Å)
Cite:SARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide
To Be Published
9HDC
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SARS-CoV-2 Main Protease in complex with (3S)-3-[(3R)-3-phenylpiperidine-1-carbonyl]indan-1-one
Descriptor: (3~{S})-3-[(3~{R})-3-phenylpiperidin-1-yl]carbonyl-2,3-dihydroinden-1-one, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Hanoulle, X, Charton, J, Deprez, B.
Deposit date:2024-11-12
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.794 Å)
Cite:SARS-CoV-2 Main Protease in complex with (3S)-3-[(3R)-3-phenylpiperidine-1-carbonyl]indan-1-one
To Be Published
9HDJ
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SARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one
Descriptor: (3~{R})-3-[(3~{R})-3-phenyl-4-(phenylmethyl)piperazin-1-yl]carbonyl-2,3-dihydroinden-1-one, 3C-like proteinase nsp5, FORMIC ACID
Authors:Hanoulle, X, Charton, J, Deprez, B.
Deposit date:2024-11-12
Release date:2024-11-27
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:SARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one
To Be Published
9HDN
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SARS-CoV-2 Main Protease in complex with (1R)-3-oxo-N-[2-oxo-2-(N-phenylanilino)ethyl]indane-1-carboxamide
Descriptor: (1~{R})-~{N}-[2-(diphenylamino)-2-oxidanylidene-ethyl]-3-oxidanylidene-1,2-dihydroindene-1-carboxamide, 3C-like proteinase nsp5
Authors:Hanoulle, X, Charton, J, Deprez, B.
Deposit date:2024-11-12
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:SARS-CoV-2 Main Protease in complex with (1R)-3-oxo-N-[2-oxo-2-(N-phenylanilino)ethyl]indane-1-carboxamide
To Be Published

238582

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