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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: more than 1 year ago)2022-09-02
9G9K
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BU of 9g9k by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR2 complex (4.3) bound to AMPNPP
Descriptor: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-01-29
Method:ELECTRON MICROSCOPY (3.34 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
8VUO
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BU of 8vuo by Molmil
Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase, 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE, ...
Authors:Misra, A, Rahisuddin, R, Gupta, Y.K.
Deposit date:2024-01-29
Release date:2025-02-05
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA
To Be Published
8Z6A
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BU of 8z6a by Molmil
Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion 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, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-18
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.99 Å)
Cite:Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation
To Be Published
8Z7B
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BU of 8z7b by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-19
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2)
To Be Published
8Z7G
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BU of 8z7g by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-20
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.06 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)
To Be Published
9CDK
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BU of 9cdk by Molmil
SARS-CoV-2 Mpro A173V mutant in complex with small molecule inhibitor Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Tang, S, Kenneson, J.R, Anderson, K.S.
Deposit date:2024-06-25
Release date:2025-02-05
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.61 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9CDL
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BU of 9cdl by Molmil
SARS-CoV-2 Mpro E166V/L50F double mutant in complex with small molecule inhibitor Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
Authors:Tang, S, Kenneson, J.R, Huynh, K, Anderson, K.S.
Deposit date:2024-06-25
Release date:2025-02-05
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.52 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9G9C
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BU of 9g9c by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR (3.2) complex
Descriptor: CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.72 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9G9D
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BU of 9g9d by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR (4.3) complex
Descriptor: CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
8XSD
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BU of 8xsd by Molmil
BA.5 Spike complex with CR9
Descriptor: CR9 heavy chain, CR9 light chain, Spike glycoprotein
Authors:Feng, L.L.
Deposit date:2024-01-09
Release date:2025-02-12
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.55 Å)
Cite:A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.
Signal Transduct Target Ther, 10, 2025
8Z6S
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BU of 8z6s by Molmil
Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1.
Descriptor: CYFN1006-1 heavy chain, CYFN1006-1 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:Wang, Y.J, Sun, L.
Deposit date:2024-04-19
Release date:2025-02-12
Method:ELECTRON MICROSCOPY (2.84 Å)
Cite:Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1.
To Be Published
8Z6W
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BU of 8z6w by Molmil
Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
Descriptor: CYFN1006-2 heavy chain, CYFN1006-2 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:Wang, Y.J, Sun, L.
Deposit date:2024-04-19
Release date:2025-02-12
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
To Be Published
8Z86
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BU of 8z86 by Molmil
BA.5 RBD in complex with CR9
Descriptor: CR9 heavy chain, CR9 light chain, Spike protein S1
Authors:Feng, L.L.
Deposit date:2024-04-21
Release date:2025-02-12
Last modified:2025-06-18
Method:ELECTRON MICROSCOPY (3.87 Å)
Cite:A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.
Signal Transduct Target Ther, 10, 2025
9BNU
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BU of 9bnu by Molmil
Crystal Structure of T190I SARS-CoV-2 Main Protease
Descriptor: 3C-like proteinase nsp5
Authors:Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BNW
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BU of 9bnw by Molmil
Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease
Descriptor: 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO7
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BU of 9bo7 by Molmil
Crystal Structure of L50F SARS-CoV-2 Main Protease 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, 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO8
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BU of 9bo8 by Molmil
Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.49 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9EX8
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BU of 9ex8 by Molmil
Free form of a mutant of SARS-CoV-2 main protease Mpro.
Descriptor: Non-structural protein 7
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-05
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EYA
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BU of 9eya by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp4/5 substrate peptide (soaking).
Descriptor: Non-structural protein 7, THR-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-ARG-LYS
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-09
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EZ4
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BU of 9ez4 by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp5/6 substrate peptide.
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLUTAMINE, ...
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-10
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EZ6
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BU of 9ez6 by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp14/15 substrate peptide.
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, DIMETHYL SULFOXIDE, ...
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-10
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9J19
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BU of 9j19 by Molmil
The crystal structure of COVID-19 main protease in complex with an inhibitor minocycline
Descriptor: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE, 3C-like proteinase nsp5
Authors:Singh, A, Jangid, K, Dhaka, P, Tomar, S, Kumar, P.
Deposit date:2024-08-04
Release date:2025-02-12
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural and Mechanistic Insights into the Main Protease (Mpro) Dimer Interface Destabilization Inhibitor: Unveiling New Therapeutic Avenues against SARS-CoV-2.
Biochemistry, 64, 2025
9LAE
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BU of 9lae by Molmil
Locally refined region of SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 3E2, Heavy chain of 9G11, ...
Authors:Jiang, Y, Sun, H, Zheng, Q, Li, S.
Deposit date:2025-01-02
Release date:2025-02-12
Last modified:2025-02-19
Method:ELECTRON MICROSCOPY (3.46 Å)
Cite:Structural insight into broadening SARS-CoV-2 neutralization by an antibody cocktail harbouring both NTD and RBD potent antibodies.
Emerg Microbes Infect, 13, 2024
8VYA
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BU of 8vya by Molmil
SARS-CoV-2 Omicron Variant Spike Glycoprotein Fusion Core (Q954H)
Descriptor: SARS-CoV-2 Omicron variant spike glycoprotein C-terminal heptad repeat domain, SARS-CoV-2 Omicron variant spike glycoprotein N-terminal heptad repeat domain (Q954H)
Authors:Outlaw, V.K, Apurba, R, Vithanage, N.
Deposit date:2024-02-07
Release date:2025-02-19
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:SARS-CoV-2 Omicron Variant Spike Glycoprotein Mutation Q954H Enhances Fusion Core Stability
to be published
8Z4W
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BU of 8z4w by Molmil
Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors
Descriptor: 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone, GLYCEROL, Non-structural protein 3, ...
Authors:Hu, H.C, Xu, Y.C.
Deposit date:2024-04-17
Release date:2025-02-26
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Nonstructural Protein Inhibitors.
J.Am.Chem.Soc., 146, 2024

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PDB entries from 2025-07-09

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