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 (4279)Repr. entries (1869)Latest entries (113)

7L7K

Cryo-EM structure of protein encoded by vaccine candidate BNT162b2
Descriptor:	Spike glycoprotein
Authors:	Lees, J.A, Han, S.
Deposit date:	2020-12-28
Release date:	2021-02-24
Last modified:	2021-04-21
Method:	ELECTRON MICROSCOPY (3.29 Å)
Cite:	BNT162b vaccines protect rhesus macaques from SARS-CoV-2. Nature, 592, 2021

7LBN

X-ray crystal structure of the SARS-CoV-2 main protease with Calpain I Inhibitor
Descriptor:	3C-like proteinase, Calpain I Inhibitor, SULFATE ION
Authors:	Narwal, M, Murakami, K.S.
Deposit date:	2021-01-08
Release date:	2021-02-24
Last modified:	2023-11-15
Method:	X-RAY DIFFRACTION (1.76 Å)
Cite:	Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay. Commun Biol, 5, 2022

7LBR

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89
Descriptor:	5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1S,3R)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide, GLYCEROL, Non-structural protein 3, ...
Authors:	Ratia, K.M, Xiong, R, Thatcher, G.R.
Deposit date:	2021-01-08
Release date:	2021-02-24
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.2 Å)
Cite:	Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures. Biorxiv, 2021

7NFV

Structure of SARS-CoV-2 Papain-like protease PLpro
Descriptor:	CHLORIDE ION, GLYCEROL, PHOSPHATE ION, ...
Authors:	Srinivasan, V, Gunther, S, Reinke, P, Werner, N, Falke, S, Brognaro, H, Ullah, N, Andaleeb, H, Perbandt, M, Alves Franca, B, Schwinzer, M, Wang, M, Sprenger, J, Lieske, J, Ginn, H, Lane, T.J, Yefanov, O, Gelisio, L, Koua, F, Saouane, S, Tolstikova, A, Groessler, M, Fleckenstein, H, Ewert, W, Trost, F, Lorenzen, K, Schubert, R, Han, H, Schmidt, C, Brings, L, Ehrt, C, Rarey, M, Galchenkova, M, Gevorkov, Y, Li, C, Perk, A, Awel, S, Hinrichs, W, Meents, A, Betzel, C.
Deposit date:	2021-02-07
Release date:	2021-02-24
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (1.42 Å)
Cite:	Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol, 5, 2022

7BEH

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab
Descriptor:	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, COVOX-316 heavy chain, ...
Authors:	Zhou, D, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2020-12-23
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.3 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7BEI

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, COVOX-150 heavy chain, ...
Authors:	Zhou, D, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2020-12-23
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.3 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7BEK

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 2)
Descriptor:	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:	Zhou, D, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2020-12-23
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.04 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7BEL

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-88 and COVOX-45 Fabs
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, COVOX-45 heavy chain, ...
Authors:	Zhou, D, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2020-12-23
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.53 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7BEM

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 scFv
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, COVOX-269 Vh domain, ...
Authors:	Zhou, D, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2020-12-24
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.52 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7BEN

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253 and COVOX-75 Fabs
Descriptor:	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, BROMIDE ION, ...
Authors:	Zhou, D, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2020-12-24
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.5 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7BEO

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253H55L and COVOX-75 Fabs
Descriptor:	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, ACETATE ION, ...
Authors:	Zhou, D, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2020-12-24
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (3.19 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7BEP

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs
Descriptor:	CHLORIDE ION, COVOX-384 heavy chain, COVOX-384 light chain, ...
Authors:	Zhou, D, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2020-12-24
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.61 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7CI3

The crystal structure of the SARS-CoV-2 ORF7a ectodomain
Descriptor:	Orf7a protein
Authors:	Zhou, Z, Zhou, Z, Chen, S.
Deposit date:	2020-07-07
Release date:	2021-03-03
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.2 Å)
Cite:	Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14 + monocytes. Iscience, 24, 2021

7LOP

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV05-163 and CR3022
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 Fab heavy chain, CR3022 Fab light chain, ...
Authors:	Yuan, M, Zhu, X, Wilson, I.A.
Deposit date:	2021-02-10
Release date:	2021-03-03
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.246 Å)
Cite:	Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Science, 373, 2021

7ND3

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-40 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, COVOX-40 heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2023-11-29
Method:	ELECTRON MICROSCOPY (3.7 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7ND4

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-88 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, COVOX-88 Fab heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2021-04-28
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7ND5

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 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, COVOX-150 Fab heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2021-04-28
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7ND6

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-40 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, COVOX-158 Fab heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2021-04-28
Method:	ELECTRON MICROSCOPY (7.3 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7ND7

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2021-04-28
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7ND8

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-384 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, COVOX-384 Fab heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2021-04-28
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7ND9

EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-253H55L 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2021-04-28
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7NDB

EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-253H165L 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2021-04-28
Method:	ELECTRON MICROSCOPY (4.6 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7NDC

EM structure of SARS-CoV-2 Spike glycoprotein (all RBD down) in complex with COVOX-159
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, COVOX-159 Fab light chain, ...
Authors:	Duyvesteyn, H.M.E, Zhao, Y, Ren, J, Stuart, D.
Deposit date:	2021-01-30
Release date:	2021-03-03
Last modified:	2021-04-28
Method:	ELECTRON MICROSCOPY (4.1 Å)
Cite:	The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell, 184, 2021

7NEG

Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody COVOX-269 Fab heavy chain, Antibody COVOX-269 Fab light chain, ...
Authors:	Zhou, D, Ren, J, Stuart, D.
Deposit date:	2021-02-04
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.19 Å)
Cite:	Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell, 184, 2021

7NEH

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab
Descriptor:	1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:	Zhou, D, Ren, J, Stuart, D.
Deposit date:	2021-02-04
Release date:	2021-03-03
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (1.77 Å)
Cite:	Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell, 184, 2021

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Total results:	1869
Displayed results:	25
Sorted by:	Release date (from oldest)