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)

8OSX

SARS-CoV-2 nsp10-16 methyltransferase in complex with ATP
Descriptor:	1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:	Kremling, V, Sprenger, J, Oberthuer, D.
Deposit date:	2023-04-20
Release date:	2023-05-31
Last modified:	2024-06-19
Method:	X-RAY DIFFRACTION (1.83 Å)
Cite:	Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16 To Be Published

7WT7

SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 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, Heavy chain of Fab 9A8, ...
Authors:	Wang, X, Wang, L.
Deposit date:	2022-02-04
Release date:	2023-06-07
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD. Cell Discov, 8, 2022

7WT8

SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 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, Heavy chain of Fab 9A8, ...
Authors:	Wang, X, Wang, L.
Deposit date:	2022-02-04
Release date:	2023-06-07
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD. Cell Discov, 8, 2022

7WT9

SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8
Descriptor:	Heavy chain of Fab 9A8, Light chain of Fab 9A8, Spike glycoprotein
Authors:	Wang, X, Wang, L.
Deposit date:	2022-02-04
Release date:	2023-06-07
Method:	ELECTRON MICROSCOPY (4.3 Å)
Cite:	A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD. Cell Discov, 8, 2022

7Y6D

Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed 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:	Xu, J, Song, Y, Li, S.
Deposit date:	2022-06-20
Release date:	2023-06-07
Method:	ELECTRON MICROSCOPY (4.39 Å)
Cite:	In situ architecture and membrane fusion of SARS-CoV-2 Delta variant. Proc.Natl.Acad.Sci.USA, 120, 2023

8D4P

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10-90-3-C1
Descriptor:	2-chloro-N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]acetamide, 3C-like proteinase
Authors:	Butler, S.G, Chen, Y, Wang, J.
Deposit date:	2022-06-02
Release date:	2023-06-07
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.04 Å)
Cite:	Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10-90-3-C1 To Be Published

8D55

Closed state of SARS-CoV-2 BA.2 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, Tang, W.C, Gao, H.L, Shi, W, Peng, H.Q, Volloch, S.R, Xiao, T.S, Chen, B.
Deposit date:	2022-06-04
Release date:	2023-06-07
Last modified:	2023-07-26
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Nat.Struct.Mol.Biol., 30, 2023

8D56

One RBD-up state of SARS-CoV-2 BA.2 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, Tang, W.C, Gao, H.L, Shi, W, Peng, H.Q, Volloch, S.R, Xiao, T.S, Chen, B.
Deposit date:	2022-06-04
Release date:	2023-06-07
Last modified:	2023-07-26
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Nat.Struct.Mol.Biol., 30, 2023

8D5A

Middle state of SARS-CoV-2 BA.2 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, Tang, W.C, Gao, H.L, Shi, W, Peng, H.Q, Volloch, S.R, Xiao, T.S, Chen, B.
Deposit date:	2022-06-04
Release date:	2023-06-07
Last modified:	2023-07-26
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Nat.Struct.Mol.Biol., 30, 2023

8SK4

Co-structure of SARS-CoV-2 (COVID-19 with covalent pyrazoline based inhibitors)
Descriptor:	2-chloro-1-[(5R)-3-phenyl-5-(quinoxalin-5-yl)-4,5-dihydro-1H-pyrazol-1-yl]ethan-1-one, 3C-like proteinase nsp5, IMIDAZOLE
Authors:	Knapp, M.S, Ornelas, E.
Deposit date:	2023-04-18
Release date:	2023-06-07
Last modified:	2023-06-14
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors. Chembiochem, 2023

8SKH

Co-structure of SARS-CoV-2 (COVID-19 with covalent pyrazoline based inhibitors
Descriptor:	2-chloro-1-[(4R,5R)-3,4,5-triphenyl-4,5-dihydro-1H-pyrazol-1-yl]ethan-1-one, 3C-like proteinase nsp5
Authors:	Knapp, M.S, Ornelas, E.
Deposit date:	2023-04-19
Release date:	2023-06-07
Last modified:	2023-06-14
Method:	X-RAY DIFFRACTION (1.882 Å)
Cite:	Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors. Chembiochem, 24, 2023

8A23

Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in complex with TO383
Descriptor:	(2R,3R,4S,5R)-2-[4-azanyl-5-(2-quinolin-3-ylethynyl)pyrrolo[2,3-d]pyrimidin-7-yl]-5-(hydroxymethyl)oxolane-3,4-diol, 2'-O-methyltransferase nsp16, GLYCEROL, ...
Authors:	Hanigovsky, M, Krafcikova, P, Klima, M, Boura, E.
Deposit date:	2022-06-02
Release date:	2023-06-14
Last modified:	2024-02-07
Method:	X-RAY DIFFRACTION (2.8 Å)
Cite:	Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in complex with TO383 To Be Published

8D34

Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A
Descriptor:	Uridylate-specific endoribonuclease nsp15
Authors:	Farraj, R.A, Edwards, R.A, Glover, J.N.M.
Deposit date:	2022-05-31
Release date:	2023-06-14
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.91 Å)
Cite:	Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A To Be Published

8DT8

LM18/Nb136 bispecific tetra-nanobody immunoglobulin in complex with SARS-CoV-2-6P-Mut7 S protein (focused refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, LM18 nanobody, Nb136 nanobody, ...
Authors:	Ozorowski, G, Turner, H.L, Ward, A.B.
Deposit date:	2022-07-25
Release date:	2023-06-14
Method:	ELECTRON MICROSCOPY (3.34 Å)
Cite:	Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins. Proc.Natl.Acad.Sci.USA, 120, 2023

8ELH

Crystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANQF from SARS-CoV-2 virus
Descriptor:	ACETATE ION, Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, ...
Authors:	Murdolo, L.D, Gras, S.
Deposit date:	2022-09-24
Release date:	2023-06-14
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.85 Å)
Cite:	A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature, 620, 2023

8EOO

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibodies WRAIR-2063 and WRAIR-2151
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Spike protein S1, ...
Authors:	Jensen, J.L, Sankhala, R.S, Joyce, M.G.
Deposit date:	2022-10-03
Release date:	2023-06-14
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.77 Å)
Cite:	Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity. J.Virol., 97, 2023

8SXO

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164I Mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
Deposit date:	2023-05-23
Release date:	2023-06-14
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (2.76 Å)
Cite:	Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164I Mutant To Be Published

7Y6L

The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab816
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Ab816 heavy chain, Ab816 light chain, ...
Authors:	Uchikubo, T, Shirouzu, M.
Deposit date:	2022-06-21
Release date:	2023-06-21
Last modified:	2023-09-13
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents. Iscience, 26, 2023

7Y6N

The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab803
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Ab803 heavy chain, Ab803 light chain, ...
Authors:	Uchikubo, T, Shirouzu, M.
Deposit date:	2022-06-21
Release date:	2023-06-21
Last modified:	2023-09-13
Method:	ELECTRON MICROSCOPY (4.4 Å)
Cite:	Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents. Iscience, 26, 2023

8EPN

Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD Down conformation
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:	Williams, J.A, Harshbarger, W.
Deposit date:	2022-10-06
Release date:	2023-06-21
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity. Sci Adv, 9, 2023

8EPP

Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs in the open conformation
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:	Williams, J.A, Harshbarger, W.
Deposit date:	2022-10-06
Release date:	2023-06-21
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity. Sci Adv, 9, 2023

8EPQ

Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs exposed
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:	Williams, J.A, Harshbarger, W.
Deposit date:	2022-10-06
Release date:	2023-06-21
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity. Sci Adv, 9, 2023

8HUR

Crystal structure of SARS-Cov-2 main protease in complex with S217622
Descriptor:	3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:	Zhou, X.L, Zhang, J, Li, J.
Deposit date:	2022-12-24
Release date:	2023-06-21
Last modified:	2024-02-07
Method:	X-RAY DIFFRACTION (1.64 Å)
Cite:	Structural basis for the inhibition of coronaviral main proteases by ensitrelvir. Structure, 31, 2023

8HUV

Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with S217622
Descriptor:	3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:	Zeng, P, Zhang, J, Li, J.
Deposit date:	2022-12-24
Release date:	2023-06-21
Last modified:	2024-02-07
Method:	X-RAY DIFFRACTION (1.97 Å)
Cite:	Structural basis for the inhibition of coronaviral main proteases by ensitrelvir. Structure, 31, 2023

8HUW

Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with S217622
Descriptor:	3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:	Wang, J, Zhang, J, Li, J.
Deposit date:	2022-12-24
Release date:	2023-06-21
Last modified:	2024-02-07
Method:	X-RAY DIFFRACTION (1.75 Å)
Cite:	Structural basis for the inhibition of coronaviral main proteases by ensitrelvir. Structure, 31, 2023

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Total results:	4406
Displayed results:	25
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