Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

COVID-19 featured content

This page is also available in: 日本語简体中文繁體中文한국어
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)
9CPY
DownloadVisualize
BU of 9cpy by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-0860 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, C11-0860 Fab heavy chain, C11-0860 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9P0F
DownloadVisualize
BU of 9p0f by Molmil
Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
Descriptor: Non-structural protein 4, SODIUM ION
Authors:Minasov, G, Shuvalova, L, Brunzelle, J.S, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:2025-06-06
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
To Be Published
9CFE
DownloadVisualize
BU of 9cfe by Molmil
Cryo-EM Local Refinement of Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFF
DownloadVisualize
BU of 9cff by Molmil
Cryo-EM Refinement of Antibody 19-77 in complex with SARS-CoV-2 HK.3 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFG
DownloadVisualize
BU of 9cfg by Molmil
Cryo-EM Refinement of Antibody 19-77 R71V in complex with SARS-CoV-2 HK.3 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9CFH
DownloadVisualize
BU of 9cfh by Molmil
Cryo-EM Refinement of Antibody 19-77 R71V in complex with SARS-CoV-2 JD.1.1 RBD
Descriptor: Spike protein S1, heavy chain, light chain
Authors:Casner, R.G, Shapiro, L.
Deposit date:2024-06-27
Release date:2025-07-02
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:More SARS-CoV-2 antibodies
To Be Published
9J8T
DownloadVisualize
BU of 9j8t by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with Mp-4L2
Descriptor: 3C-like proteinase nsp5, TYR-DSG-DLE-DPN-DGN-ARG-DTH-DAS-DTR-DTH-ALO-DGN-DTY-CCJ-GLY-NH2
Authors:Shi, Y.S, Yang, J.Y, Wang, M.W.
Deposit date:2024-08-21
Release date:2025-07-02
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:De novo discovery of a non-covalent cell-penetrating bicyclic peptide inhibitor targeting SARS-CoV-2 main protease
To Be Published
9J8U
DownloadVisualize
BU of 9j8u by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with Mp-4D7
Descriptor: 3C-like proteinase nsp5, DTY-VAL-THR-PHE-HIS-ALO-2TL-2TL-PRO-PHE-LEU-DPR-PRO-CCJ-GLY-NH2
Authors:Shi, Y.S, Yang, J.Y, Wang, M.W.
Deposit date:2024-08-21
Release date:2025-07-02
Method:X-RAY DIFFRACTION (2.71 Å)
Cite:De novo discovery of a non-covalent cell-penetrating bicyclic pep-tide inhibitor targeting SARS-CoV-2 main protease
To Be Published
9P6P
DownloadVisualize
BU of 9p6p by Molmil
Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
Descriptor: 2'-O-methyltransferase, 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ...
Authors:Minasov, G, Shuvalova, L, Maltseva, N, Kim, Y, Kiryukhina, O, Joachimiak, A, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:2025-06-19
Release date:2025-07-02
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
To Be Published
9CJP
DownloadVisualize
BU of 9cjp by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 1,2-ETHANEDIOL, 3C-like proteinase nsp5, ...
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir
To Be Published
9CJQ
DownloadVisualize
BU of 9cjq by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir
Descriptor: 1,2-ETHANEDIOL, 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, main protease
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.24 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir
To Be Published
9CJR
DownloadVisualize
BU of 9cjr by Molmil
X-ray crystal structure of SARS-CoV-2 main protease double mutants in complex with Ensitrelvir
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, CHLORIDE ION, ...
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease double mutants in complex with Ensitrelvir
To Be Published
9CJS
DownloadVisualize
BU of 9cjs by Molmil
X-ray crystal structure of SARS-CoV-2 main protease triple mutants in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease triple mutants in complex with Bofutrelvir
To Be Published
9E9Q
DownloadVisualize
BU of 9e9q by Molmil
SARS-CoV-2 SL5 crystal structure native
Descriptor: MAGNESIUM ION, RNA (101-MER)
Authors:Jones, C.P, Ferre-D'Amare, A.R.
Deposit date:2024-11-08
Release date:2025-07-09
Method:X-RAY DIFFRACTION (3.33 Å)
Cite:Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.
Rna, 31, 2025
9MPW
DownloadVisualize
BU of 9mpw by Molmil
SARS-CoV2 Spike S2 Subunit in complex with M15 Antibody Fragment
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab M15 Heavy Chain, ...
Authors:Sapse, I.A, Bajic, G.
Deposit date:2024-12-31
Release date:2025-07-09
Method:ELECTRON MICROSCOPY (3.37 Å)
Cite:SARS-CoV2 Spike S2 Subunit in complex with M15 Antibody Fragment
To Be Published
9RCZ
DownloadVisualize
BU of 9rcz by Molmil
Structure of the N-terminal domain of non-structural protein 1 (Nsp1) from SARS-CoV-2
Descriptor: ORF1a polyprotein
Authors:Lennartz, F, Weiss, M.S.
Deposit date:2025-05-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Crystallographic fragment screening against SARS-CoV-2 Nsp1 using the F2X-Entry Screen and a newly developed fragment library.
To Be Published

238582

PDB entries from 2025-07-09

PDB statisticsPDBj update infoContact PDBjnumon