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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
All entries (5197)Repr. entries (2266)Latest entries (44)
9FCM
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BU of 9fcm by Molmil
Single-domain antibody binding the SARS-COV2 S2
Descriptor: CHLORIDE ION, Single-domain antibody R3DC23, Spike protein S2'
Authors:Vann Molle, I, Remaut, H.
Deposit date:2024-05-15
Release date:2025-05-21
Last modified:2025-06-11
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that clamp the spike at its base.
Nat Commun, 16, 2025
9UJ2
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BU of 9uj2 by Molmil
14-3-3 zeta chimera with the S202R peptide of SARS-CoV-2 N (residues 200-213)
Descriptor: 1,2-ETHANEDIOL, 14-3-3 protein zeta/delta,Peptide from Nucleoprotein, DI(HYDROXYETHYL)ETHER
Authors:Boyko, K.M, Matyuta, I.O, Minyaev, M.E, Perfilova, K.V, Sluchanko, N.N.
Deposit date:2025-04-16
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness.
Biochem.Biophys.Res.Commun., 767, 2025
9ELE
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BU of 9ele by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 RBD in complex with human ACE2 (local refinement of RBD and hACE2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (3.16 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELF
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BU of 9elf by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with human 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, Processed angiotensin-converting enzyme 2, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.88 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELG
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BU of 9elg by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike RBD and NTD (local refinement of RBD and NTD)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (3.71 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELH
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BU of 9elh by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (one RBD up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.98 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELI
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BU of 9eli by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (closed state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.82 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELN
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BU of 9eln by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+S31 deletion spike protein (one RBD up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELO
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BU of 9elo by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+S31 deletion spike protein (closed state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.74 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELP
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BU of 9elp by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11.1+S31 deletion spike protein (one RBD up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.94 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELQ
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BU of 9elq by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11.1+S31 deletion spike protein (closed state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.64 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9HH5
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BU of 9hh5 by Molmil
Crystal Structure of nsp15 Endoribonuclease from SARS CoV-2 in Complex with Sepantronium (YM-155)
Descriptor: 1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl)benzo[f]benzimidazol-3-ium-4,9-dione, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Nsp15 - Uridylate-specific endoribonuclease, ...
Authors:Chatziefthymiou, S.D, Kolbe, M, Hakanpaeae, J, Labahn, J, Windshuegel, B.
Deposit date:2024-11-21
Release date:2025-05-28
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15.
Protein Sci., 34, 2025
9HH6
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BU of 9hh6 by Molmil
Crystal Structure of Nsp15 Endoribonuclease from SARS CoV-2 in Complex with TAS-103
Descriptor: 1,2-ETHANEDIOL, 6-[2-(dimethylamino)ethylamino]-3-oxidanyl-indeno[2,1-c]quinolin-7-one, ORF1ab polyprotein, ...
Authors:Chatziefthymiou, S.D, Kolbe, M, Hakanpaeae, J, Labahn, J, Windshuegel, B.
Deposit date:2024-11-21
Release date:2025-05-28
Method:SOLUTION SCATTERING (2 Å), X-RAY DIFFRACTION
Cite:Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15.
Protein Sci., 34, 2025
9IZB
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BU of 9izb by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with TMP1
Descriptor: 3C-like proteinase nsp5, TMP1
Authors:Deng, X.Y, Zeng, R, Yang, S.Y, Lei, J.
Deposit date:2024-08-01
Release date:2025-05-28
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal structure of SARS-CoV-2 main protease in complex with TMP1
To Be Published
9ELJ
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BU of 9elj by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (one RBD up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (2.92 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELK
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BU of 9elk by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (closed state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (2.82 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELL
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BU of 9ell by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (one RBD up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELM
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BU of 9elm by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (closed state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (2.68 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ML4
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BU of 9ml4 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-A10 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-A10 heavy chain, M8b-A10 light chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML5
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BU of 9ml5 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-B8 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, M8b-B8 heavy chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML6
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BU of 9ml6 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C9 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-C9 heavy chain, M8b-C9 light chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML7
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BU of 9ml7 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C10 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, M8b-C10 heavy chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML8
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BU of 9ml8 by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-B1 heavy chain, M8b-B1 light chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML9
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BU of 9ml9 by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab
Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-C9 heavy chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:X-RAY DIFFRACTION (2.59 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9MRU
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BU of 9mru by Molmil
Structural Asymmetry in SARS-CoV-2 Nsp15 Hexamer Important for Catalytic Activity
Descriptor: Uridylate-specific endoribonuclease nsp15
Authors:Ketawala, G.K, Sonowal, M, Schrag, L, Fromme, R, Botha, S, Fromme, P.
Deposit date:2025-01-08
Release date:2025-06-04
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structural Asymmetry in SARS-CoV-2 Nsp15 Hexamer Important for Catalytic Activity
To Be Published

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