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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: 3 weeks ago)2021-05-29
7EK6

Structure of viral peptides IPB19/N52
Descriptor: Spike protein S2
Authors:Yu, D, Qin, B, Cui, S, He, Y.
Deposit date:2021-04-04
Release date:2021-06-09
Method:X-RAY DIFFRACTION (1.243 Å)
Cite:Structure-based design and characterization of novel fusion-inhibitory lipopeptides against SARS-CoV-2 and emerging variants.
Emerg Microbes Infect, 2021
7EQ4

Crystal Structure of the N-terminus of Nonstructural protein 1 from SARS-CoV-2
Descriptor: Host translation inhibitor nsp1
Authors:Liu, Y, Ke, Z, Hu, H, Zhao, K, Xiao, J, Xia, Y, Li, Y.
Deposit date:2021-04-29
Release date:2021-06-09
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Structural basis and function of the N-terminus of SARS-CoV-2 nonstructural protein 1
To Be Published
5SAG

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-1605072
Descriptor: 3-(1H-imidazol-2-yl)propan-1-amine, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (1.881 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SA9

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2697514548
Descriptor: 1-methylindazole-3-carboxamide, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SAD

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z425449682
Descriptor: (3-phenyl-1,2-oxazol-5-yl)methylazanium, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (1.961 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SAI

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1424343998
Descriptor: N-{2-[(propan-2-yl)sulfanyl]phenyl}urea, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.022 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SAC

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z59181945
Descriptor: CITRIC ACID, N-hydroxyquinoline-2-carboxamide, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.029 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SA4

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z239136710
Descriptor: N-(5-methyl-1H-pyrazol-3-yl)acetamide, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.046 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SA5

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1530301542
Descriptor: 4-ethyl-2-(1H-imidazol-5-yl)-1,3-thiazole, CITRIC ACID, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SAF

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-321461
Descriptor: 6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidine, CITRIC ACID, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.11 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SAE

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z3219959731
Descriptor: CITRIC ACID, Uridylate-specific endoribonuclease, pyridazin-3(2H)-one
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SAH

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-100112
Descriptor: 2-methyl-5,6,7,8-tetrahydropyrido[4,3-c]pyridazin-3(2H)-one, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.16 Å)
Cite:PanDDA analysis group deposition
To Be Published
7N0I

Structure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2
Descriptor: ACETATE ION, MAGNESIUM ION, Nucleoprotein, ...
Authors:Ye, Q, Corbett, K.D.
Deposit date:2021-05-25
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2
To Be Published
5SA7

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1673618163
Descriptor: 4-amino-N-(2-hydroxyethyl)-N-methylbenzene-1-sulfonamide, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.222 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SAA

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284
Descriptor: 3-[(2S)-1-(methanesulfonyl)pyrrolidin-2-yl]-5-methyl-1,2-oxazole, CITRIC ACID, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.239 Å)
Cite:PanDDA analysis group deposition
To Be Published
5SA8

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z68299550
Descriptor: 3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.298 Å)
Cite:PanDDA analysis group deposition
To Be Published
7DJZ

Crystal structure of SARS-CoV-2 Spike RBD in complex with MW01 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CITRIC ACID, MW01 heavy chain, ...
Authors:Wang, J, Jiao, S, Wang, R, Zhang, J, Zhang, M, Wang, M.
Deposit date:2020-11-22
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.397 Å)
Cite:Antibody-dependent enhancement (ADE) of SARS-CoV-2 infection requires FcgammaRIIB-mediated uptake of virus-antibody complex with bivalent interaction
To Be Published
7E7Y

Crystal structure of the SARS-CoV-2 S RBD in complex with BD-623 Fab
Descriptor: BD-623 Fab H, BD-623 Fab L, Spike protein S1
Authors:Wei, Y, Xiao, J.
Deposit date:2021-02-28
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.41 Å)
Cite:Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.
Cell Res., 2021
5SAB

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z31504642
Descriptor: 2-methoxy-N-phenylacetamide, CITRIC ACID, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.486 Å)
Cite:PanDDA analysis group deposition
To Be Published
7N33

SARS-CoV-2 Nsp15 endoribonuclease pre-cleavage state
Descriptor: RNA (5'-R(*A)-D(*(UFT))-R(P*A)-3'), Uridylate-specific endoribonuclease
Authors:Frazier, M.N, Dillard, L.B, Krahn, J.M, Stanley, R.E.
Deposit date:2021-05-31
Release date:2021-06-09
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Characterization of SARS2 Nsp15 Nuclease Activity Reveals its Mad About U
To Be Published
5SA6

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2856434783
Descriptor: N-benzyl-1-(4-fluorophenyl)methanamine, Uridylate-specific endoribonuclease
Authors:Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:2021-05-19
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.517 Å)
Cite:PanDDA analysis group deposition
To Be Published
7N0S

Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody B6
Descriptor: Nucleoprotein, Single-domain antibody B6
Authors:Corbett, K.D, Ye, Q.
Deposit date:2021-05-26
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.56 Å)
Cite:Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody B6
To Be Published
7E7X

SARS-CoV-2 Spike Protein N terminal domain in Complex with N11 Fab
Descriptor: N11 Fab Light chain, N11 Fab heavy chain, Spike protein S1
Authors:Zhang, Z, Shuo, D, Xiao, J.
Deposit date:2021-02-28
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.78 Å)
Cite:Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.
Cell Res., 2021
7E86

Crystal structure of the SARS-CoV-2 S RBD in complex with BD-508 Fab
Descriptor: BD-508 Fab Heavy Chain, BD-508 Fab Light Chain, Spike protein S1
Authors:Gao, C, Xiao, J.
Deposit date:2021-03-01
Release date:2021-06-09
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.
Cell Res., 2021
7E88

Crystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab
Descriptor: BD-515 Fab Heavy Chain, BD-515 Fab Light Chain, Spike protein S1
Authors:Gao, C, Wei, Y, Xiao, J.
Deposit date:2021-03-01
Release date:2021-06-09
Method:X-RAY DIFFRACTION (3.14 Å)
Cite:Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines.
Cell Res., 2021

 

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PDB entries from 2021-06-09