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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
9IN1
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BU of 9in1 by Molmil
Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2
Descriptor: Nucleoprotein
Authors:Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
Deposit date:2024-07-05
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
J.Struct.Biol., 217, 2025
9KSH
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BU of 9ksh by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with compound 1
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-pyridin-3-yl-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-29
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9KSJ
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BU of 9ksj by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with compound 8
Descriptor: 3-[[(6E)-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-[5-(2-methoxyethoxy)pyridin-3-yl]-2,4-bis(oxidanylidene)-1,3,5-triazinan-1-yl]methyl]-4-methyl-benzenecarbonitrile, 3C-like proteinase nsp5
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-29
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9LBS
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BU of 9lbs by Molmil
Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of ConBA-998, Heavy chain of S304 Fab, ...
Authors:Zhang, Z, Ju, B, Liu, C.
Deposit date:2025-01-03
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.41 Å)
Cite:Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs
To Be Published
9LDS
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BU of 9lds by Molmil
Crystal structure of nanobody H145 bound to SARS-CoV-2 spike stem-helix
Descriptor: H145, Spike protein S2'
Authors:Lu, G.W, Guo, L.Y, Lin, S.
Deposit date:2025-01-06
Release date:2025-04-02
Last modified:2025-07-02
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural basis and mode of action for two broadly neutralizing nanobodies targeting the highly conserved spike stem-helix of sarbecoviruses including SARS-CoV-2 and its variants.
Plos Pathog., 21, 2025
9LYO
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BU of 9lyo by Molmil
Alpha SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, REGN10987 Fab homologue (Heavy chain), ...
Authors:Kocharovskaya, M.V, Pichkur, E.B, Shenkarev, Z.O, Lyukmanova, E.N.
Deposit date:2025-02-20
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.07 Å)
Cite:Structure and dynamics of Alpha B.1.1.7 SARS-CoV-2 S-protein in complex with Fab of neutralizing antibody REGN10987.
Biochem.Biophys.Res.Commun., 755, 2025
9LYP
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BU of 9lyp by Molmil
Alpha SARS-CoV-2 spike protein RBD-down in complex with REGN10987 Fab homologue (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, REGN10987 Fab homologue (Heavy chain), REGN10987 Fab homologue (Light chain), ...
Authors:Kocharovskaya, M.V, Pichkur, E.B, Shenkarev, Z.O, Lyukmanova, E.N.
Deposit date:2025-02-20
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structure and dynamics of Alpha B.1.1.7 SARS-CoV-2 S-protein in complex with Fab of neutralizing antibody REGN10987.
Biochem.Biophys.Res.Commun., 755, 2025
8YWY
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BU of 8ywy by Molmil
Crystal structure of SARS-Cov-2 main protease E166N mutant 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:Zhou, X.L, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-04-01
Release date:2025-04-09
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
8YWZ
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BU of 8ywz by Molmil
Crystal structure of SARS-Cov-2 main protease H163A mutant 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:Zou, X.F, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-04-01
Release date:2025-04-09
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9INL
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BU of 9inl by Molmil
Crystal structure of SARS-Cov-2 main protease E166R mutant in complex with Bofutrelvir
Descriptor: Replicase polyprotein 1a, ~{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:Zhou, X.L, Li, J.
Deposit date:2024-07-08
Release date:2025-04-09
Method:X-RAY DIFFRACTION (2.04 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9LUF
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BU of 9luf by Molmil
Crystal structure of SARS-Cov-2 main protease S144A mutant in complex with Bofutrelvir
Descriptor: ORF1a polyprotein, ~{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:Zhou, X.L, Li, J.
Deposit date:2025-02-08
Release date:2025-04-09
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9LUG
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BU of 9lug by Molmil
Crystal structure of SARS-Cov-2 main protease E166V mutant in complex with Bofutrelvir
Descriptor: ORF1a polyprotein, ~{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:Zhou, X.L, Li, J.
Deposit date:2025-02-08
Release date:2025-04-09
Method:X-RAY DIFFRACTION (2.13 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9B4X
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BU of 9b4x by Molmil
SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation (SPIKE-AXA)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-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)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-03-21
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (3.33 Å)
Cite:Cryo-EM structure of SARS CoV-2 full-length spike with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation
To Be Published
9B9U
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BU of 9b9u by Molmil
SARS-CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation (SPIKE-KXK)
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:Singh, S, Hasan, S.S.
Deposit date:2024-04-03
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.86 Å)
Cite:SARS CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation
To Be Published
9BD9
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BU of 9bd9 by Molmil
SARS CoV-2 full-length WT spike protein, 1RBD-up conformation (SPIKE-WT)
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:Singh, S, Hasan, S.S.
Deposit date:2024-04-11
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.95 Å)
Cite:Structure of SARS CoV-2 full-length spike protein, 1RBD-up conformation
To Be Published
9DHY
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BU of 9dhy by Molmil
Structure of SARS-CoV-2 spike in complex with antibody Fab COVIC-154
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody Fab COVIC-154 Heavy Chain, ...
Authors:Yu, X, Saphire, E.O.
Deposit date:2024-09-04
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:A global collaboration for systematic analysis of broad-ranging antibodies against the SARS-CoV-2 spike protein.
Cell Rep, 44, 2025
8Z2E
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BU of 8z2e by Molmil
Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD
Descriptor: 1F11-H, 1F11-L, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Wang, X.Q, Zhang, L.Q, Chen, J, Dong, H.D.
Deposit date:2024-04-12
Release date:2025-04-23
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD
To Be Published
9BC1
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BU of 9bc1 by Molmil
SARS-CoV-2 Mpro in complex with peptide mimetic inhibitor
Descriptor: 3C-like proteinase nsp5, peptide mimetic inhibitor
Authors:Afsar, M, Priscila, B, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-23
Method:X-RAY DIFFRACTION (1.72 Å)
Cite:SARS-CoV-2 Mpro in complex with peptide mimetic inhibitor
To Be Published
9KN1
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BU of 9kn1 by Molmil
Crystal structure of SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain(N-NTD) in complex with UMP
Descriptor: Nucleoprotein, PHOSPHATE ION, URIDINE-5'-MONOPHOSPHATE
Authors:Higashiura, A, Yamamoto, A, Ito, H.
Deposit date:2024-11-18
Release date:2025-04-23
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:Structural insights into nucleocapsid protein variability: Implications for PJ34 efficacy against SARS-CoV-2.
Virology, 604, 2025
8Z9L
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BU of 8z9l by Molmil
Crystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
Authors:Lan, J, Wang, C.H.
Deposit date:2024-04-23
Release date:2025-04-30
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (3.598 Å)
Cite:Molecular mechanisms of RaTG13 and SARS-CoV-2 RBD bound to Rhinolophus affinis bat ACE2.
Protein Sci., 34, 2025
8ZBF
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BU of 8zbf by Molmil
Crystal structure of the A58-T10 DNA aptamer in complex with SARS-CoV-2 N-NTD
Descriptor: DNA (40-MER), Nucleoprotein, SODIUM ION
Authors:Chen, X, Huang, L.
Deposit date:2024-04-26
Release date:2025-04-30
Last modified:2025-05-07
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Molecular characterization and broad-spectrum mechanism of coronavirus N protein aptamer
To Be Published
9DU2
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BU of 9du2 by Molmil
SARS-CoV-2 Mpro in complex with compound 7
Descriptor: 3C-like proteinase nsp5, N-[(2S)-3-cyclopropyl-1-{[(1Z,2S)-1-imino-4-(methanesulfonyl)butan-2-yl]amino}-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Bigelow, L, Tang, H, Boguslaw, N, Duda, D.M.
Deposit date:2024-10-02
Release date:2025-04-30
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Inhibition of Dimeric SARS-CoV-2 Mpro by Aldehyde and Nitrilebased Inhibitors Displays Positive Cooperativity and a Mixture of Covalent and Non-covalent Binding.
To Be Published
9FM4
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BU of 9fm4 by Molmil
Dynamic structure of the apical stem loop of the stem loop 2 motif (s2m) from SCoV-2 Delta variant.
Descriptor: RNA (25-MER)
Authors:Wirtz Martin, M.A, Matzel, T, Makowski, J, Kensinger, A, Herr, A, Wacker, A, Richter, C, Jonker, H.R.A, Evanseck, J, Schwalbe, H.
Deposit date:2024-06-05
Release date:2025-05-07
Last modified:2025-06-04
Method:SOLUTION NMR, SOLUTION SCATTERING
Cite:Characterization of structure and dynamics of the apical stem loop of s2m from SCoV-2 Delta by NMR spectroscopy, validated by MD and SAXS
To Be Published
8X1X
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BU of 8x1x by Molmil
SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid
Descriptor: (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid, GLYCEROL, Papain-like protease nsp3, ...
Authors:Choudhary, S, Verma, S, Kumar, P, Tomar, S.
Deposit date:2023-11-09
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid
To Be Published
9BLF
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BU of 9blf by Molmil
SARS-CoV-2 core polymerase complex inhibited by araCTP
Descriptor: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one, MAGNESIUM ION, Non-structural protein 7, ...
Authors:Anderson, T.K, Kirchdeorfer, R.N.
Deposit date:2024-04-30
Release date:2025-05-14
Method:ELECTRON MICROSCOPY (3.31 Å)
Cite:Structure of the SARS-CoV-2 core-RTC bound to RNA, araCMP, and araCTP
To Be Published

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