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 (5197)Repr. entries (2266)Latest entries (44)

8J1Q

CryoEM structure of SARS CoV-2 RBD and Aptamer complex
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, AM032-0, AM047-0, ...
Authors:	Rahman, M.S, Jang, S.K, Lee, J.O.
Deposit date:	2023-04-13
Release date:	2023-06-21
Last modified:	2024-11-20
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection. Molecules, 28, 2023

8J26

CryoEM structure of SARS CoV-2 RBD and Aptamer complex
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, AM032-4, AM047-6, ...
Authors:	Rahman, M.S, Jang, S.K, Lee, J.O.
Deposit date:	2023-04-14
Release date:	2023-06-21
Last modified:	2024-11-20
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection. Molecules, 28, 2023

7YTN

Crystal structure of SARS-CoV-2 Alpha RBD in complex with the D27LEY neutralizing antibody Fab fragment
Descriptor:	Heavy chain of Fab, Light chain of Fab, Spike protein S1
Authors:	Jeong, B.S, Jeon, J.Y, Oh, B.H.
Deposit date:	2022-08-15
Release date:	2023-06-28
Last modified:	2024-10-30
Method:	X-RAY DIFFRACTION (3.51 Å)
Cite:	Structural basis for the broad and potent cross-reactivity of an N501Y-centric antibody against sarbecoviruses. Front Immunol, 13, 2022

7YVE

Omicron BA.4/5 SARS-CoV-2 S in complex with TH027 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TH027 Fab heavy chain, ...
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-06-18
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVF

Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH027 Fab
Descriptor:	Spike glycoprotein, TH027 Fab heavy chain, TH027 Fab light chain
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVG

Omicron BA.4/5 SARS-CoV-2 S in complex with TH132 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TH132 Fab heavy chain, ...
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVH

Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH132 Fab
Descriptor:	Spike glycoprotein, TH132 Fab heavy chain, TH132 Fab light chain
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVI

Omicron BA.4/5 SARS-CoV-2 S in complex with TH236 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TH236 Fab heavy chain, ...
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.7 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVJ

Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH236 Fab
Descriptor:	Spike glycoprotein, TH236 Fab heavy chain, TH236 Fab light chain
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVK

Omicron BA.4/5 SARS-CoV-2 S in complex with TH272 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TH272 Fab heavy chain, ...
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVL

Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH272 Fab
Descriptor:	Spike glycoprotein, TH272 Fab heavy chain, TH272 Fab light chain
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-06-18
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVM

Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH272 Fab
Descriptor:	Spike glycoprotein, TH281 Fab heavy chain, TH281 Fab light chain
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVN

Omicron BA.4/5 SARS-CoV-2 S in complex with TH281 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TH281 Fab heavy chain, ...
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-06-25
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVO

Omicron BA.4/5 SARS-CoV-2 S in complex with TH027/132 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TH132 Fab heavy chain, ...
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7YVP

Omicron BA.4/5 SARS-CoV-2 S in complex with TH272/281 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TH272 Fab heavy chain, ...
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-19
Release date:	2023-06-28
Last modified:	2025-06-18
Method:	ELECTRON MICROSCOPY (3.8 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

7Z8O

Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
Descriptor:	2,4,6-tris(chloromethyl)-1,3,5-triazine, GLYCEROL, Spike protein S1, ...
Authors:	Brear, P, Chen, L, Gaynor, K, Harman, M, Dods, R, Hyvonen, M.
Deposit date:	2022-03-18
Release date:	2023-06-28
Last modified:	2024-02-07
Method:	X-RAY DIFFRACTION (0.96 Å)
Cite:	Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2. Nat Commun, 14, 2023

8AAA

Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
Descriptor:	1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one, Spike protein S1, Stapled peptide
Authors:	Brear, P, Chen, L, Gaynor, K, Harman, M, Dods, R, Hyvonen, M.
Deposit date:	2022-06-30
Release date:	2023-06-28
Last modified:	2024-10-23
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2. Nat Commun, 14, 2023

8BON

Structure of the SARS-CoV-2 spike glycoprotein in complex with the macrocyclic peptide S1B3inL1
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Macrocyclic peptide S1B3inL1, ...
Authors:	Hurdiss, D.L.
Deposit date:	2022-11-15
Release date:	2023-06-28
Last modified:	2023-07-05
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein. Proc.Natl.Acad.Sci.USA, 120, 2023

8DDL

SARS-CoV-2 Main Protease (Mpro) H163A Mutant Apo Structure
Descriptor:	1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, ORF1a polyprotein, ...
Authors:	Tran, N, McLeod, M.J, Kalyaanamoorthy, S, Ganesan, A, Holyoak, T.
Deposit date:	2022-06-18
Release date:	2023-06-28
Last modified:	2024-11-13
Method:	X-RAY DIFFRACTION (1.95 Å)
Cite:	The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nat Commun, 14, 2023

8E1G

SARS-CoV-2 RBD in complex with Omicron-neutralizing antibody 2A10
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2A10 Fab, heavy chain, ...
Authors:	Wasserman, H, Hastie, K.M, Buck, T.K, Saphire, E.O.
Deposit date:	2022-08-10
Release date:	2023-06-28
Last modified:	2024-11-13
Method:	X-RAY DIFFRACTION (2.57 Å)
Cite:	Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence. Cell Rep, 42, 2023

8GOU

Omicron BA.4/5 SARS-CoV-2 S in complex with TH003 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, TH003 Fab heavy chain, ...
Authors:	Guo, Y, Zhang, G, Liang, J, Liu, F, Rao, Z.
Deposit date:	2022-08-25
Release date:	2023-06-28
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.7 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

8GPY

Crystal structure of Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv
Descriptor:	Spike protein S1, scFv
Authors:	Gao, Y.X, Song, Z.D, Wang, W.M, Guo, Y.
Deposit date:	2022-08-27
Release date:	2023-06-28
Last modified:	2024-10-23
Method:	X-RAY DIFFRACTION (2.51 Å)
Cite:	Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun, 14, 2023

8SMT

Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, WRAIR-2134 Fab heavy chain, ...
Authors:	Sankhala, R.S, Jensen, J.L, Joyce, M.G.
Deposit date:	2023-04-26
Release date:	2023-06-28
Last modified:	2024-11-06
Method:	X-RAY DIFFRACTION (3.16 Å)
Cite:	Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain. Structure, 32, 2024

7YC5

Cryo-EM structure of SARS-CoV-2 spike in complex with K202.B bispecific antibody
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Bispecific anitybody (scFv and light chain of the antibody), Heavy chain from K202.B antibody, ...
Authors:	Yoo, Y, Cho, H.S.
Deposit date:	2022-06-30
Release date:	2023-07-05
Last modified:	2025-03-05
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Novel bispecific human antibody platform specifically targeting a fully open spike conformation potently neutralizes multiple SARS-CoV-2 variants Antiviral Res., 212, 2023

7YCO

Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Repebody (A6), Spike protein S1
Authors:	Kim, U.J, Cho, H.S.
Deposit date:	2022-07-01
Release date:	2023-07-05
Last modified:	2024-10-09
Method:	X-RAY DIFFRACTION (1.96 Å)
Cite:	Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody To Be Published

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