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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
9BJ4
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Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C952
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C952 Heavy Chain, C952 Light Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9CSS
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Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, 1UP RBD 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, 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:2024-07-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.72 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9CT2
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Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, All RBD down conformation, State-3
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:Singh, S, Hasan, S.S.
Deposit date:2024-07-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9CVH
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Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, 1RBD UP, State-2
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-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-07-29
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.76 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9CXE
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SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation -C1
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:2024-07-31
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.48 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9HAJ
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Structure of compound 1 bound to SARS-CoV-2 main protease
Descriptor: (5~{R})-4-[(4-bromanyl-2-ethyl-phenyl)methyl]-1-(5-chloranylpyridin-3-yl)carbonyl-~{N}-ethyl-1,4-diazepane-5-carboxamide, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Mac Sweeney, A, Hazemann, J.
Deposit date:2024-11-04
Release date:2025-03-05
Last modified:2025-05-07
Method:X-RAY DIFFRACTION (1.276 Å)
Cite:Accelerating the Hit-To-Lead Optimization of a SARS-CoV-2 Mpro Inhibitor Series by Combining High-Throughput Medicinal Chemistry and Computational Simulations.
J.Med.Chem., 68, 2025
9I81
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SARS-CoV-2 RdRp bound to a stack of three HeE1-2Tyr molecules
Descriptor: N-[8-(cyclohexyloxy)-1-oxo-2-phenyl-1H-pyrido[2,1-b][1,3]benzothiazole-4-carbonyl]-L-tyrosine, Non-structural protein 7, Non-structural protein 8, ...
Authors:Kabinger, F, Doze, V, Schmitzova, J, Lidschreiber, M, Dienemann, C, Cramer, P.
Deposit date:2025-02-04
Release date:2025-03-05
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (2.98 Å)
Cite:Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr.
Proc.Natl.Acad.Sci.USA, 122, 2025
8U40
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Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor
Descriptor: 3C-like proteinase nsp5, N-[(2S)-3-cyclopropyl-1-({(1E,2R)-1-imino-3-[(3R)-2-oxo-2,3-dihydropyridin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]-5,7-difluoro-1H-indole-2-carboxamide
Authors:Chen, P, Arutyunova, E, Lu, J, Young, H.S, Lemieux, M.J.
Deposit date:2023-09-08
Release date:2025-03-12
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of main protease of SARS-CoV-2 complexed with inhibitor
To Be Published
8YK4
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Structure of SARS-CoV-2 RBD and antibody NT-108
Descriptor: Spike protein S1, antibody NT-108, single chain Fv fragment
Authors:Anraku, Y, Kita, S, Onodera, T, Sato, A, Tadokoro, T, Adachi, Y, Ito, S, Suzuki, T, Sasaki, J, Shiwa, N, Iwata, N, Nagata, N, Kazuki, Y, Oshimura, M, Sasaki, M, Orba, Y, Suzuki, T, Sawa, H, Hashiguchi, T, Fukuhara, H, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-04
Release date:2025-03-12
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structural Basis for Potent Neutralization Activity of SARS-CoV-2 Antibody, NT-108
To Be Published
8YKG
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BU of 8ykg by Molmil
Structure of SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (1-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, NT-108 scFv, ...
Authors:Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-05
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.28 Å)
Cite:Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
8YKH
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BU of 8ykh by Molmil
Structure of SARS-CoV-2 spike RBD in complex with NT-108 scFv
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NT-108 scFv, Spike glycoprotein
Authors:Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-05
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.27 Å)
Cite:Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
9BLL
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BU of 9bll by Molmil
Cryo-EM of RBD(EG5.1)/1301B7 Fab Complex
Descriptor: 1301B7 Heavy Chain, 1301B7 Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Walter, M.R, Green, T.J.
Deposit date:2024-04-30
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:Potent neutralization by a RBD antibody with broad specificity for SARS-CoV-2 JN.1 and other variants.
Npj Viruses, 2, 2024
9CCI
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BU of 9cci by Molmil
Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, M39 Fab heavy chain, M39 Fab light chain, ...
Authors:Bajic, G, Jaiswal, D.
Deposit date:2024-06-21
Release date:2025-03-12
Last modified:2025-05-28
Method:ELECTRON MICROSCOPY (2.65 Å)
Cite:Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.
Biorxiv, 2024
9CCJ
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BU of 9ccj by Molmil
Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, M2 Fab Heavy Chain, ...
Authors:Bajic, G, Civljak, A.
Deposit date:2024-06-21
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (2.37 Å)
Cite:Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.
Biorxiv, 2024
9CGV
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BU of 9cgv by Molmil
SARS-CoV-2 nsp12 NiRAN domain bound to a covalent inhibitor SW090466-1
Descriptor: MANGANESE (II) ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Osinski, A, Hernandez, G, Tagliabracci, V.S.
Deposit date:2024-07-01
Release date:2025-03-12
Last modified:2025-04-23
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine.
J.Biol.Chem., 301, 2025
9J66
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BU of 9j66 by Molmil
Cryo-EM structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment CAV-C65 (local refinement)
Descriptor: CAV-C65 Heavy chain, CAV-C65 Light chain, Spike protein S1
Authors:Jing, X, Chen, Y, Gong, P.
Deposit date:2024-08-15
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.55 Å)
Cite:IgA class switching enhances neutralizing potency against SARS-CoV-2 by increased antibody hinge flexibility.
Antiviral Res., 235, 2025
9N55
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BU of 9n55 by Molmil
X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
Descriptor: N-OCTANE, ORF9b protein
Authors:San Felipe, C.J, Fraser, J.S.
Deposit date:2025-02-03
Release date:2025-03-12
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
To Be Published
8UTC
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BU of 8utc by Molmil
HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
Descriptor: Beta-2-microglobulin, CHLORIDE ION, HLA class I histocompatibility antigen, ...
Authors:Oltean, N, Nyovanie, S, Hashem, A, Patskovska, L, Patskovsky, Y, Krogsgaard, M.
Deposit date:2023-10-30
Release date:2025-03-19
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
To Be Published
8Z1H
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BU of 8z1h by Molmil
Crystal structure of SARS main protease in complex with PF-00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Lin, C, Zhang, J, Li, J.
Deposit date:2024-04-11
Release date:2025-03-19
Method:X-RAY DIFFRACTION (2.61 Å)
Cite:Crystal structure of SARS main protease in complex with PF-00835231
To Be Published
9DJ8
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BU of 9dj8 by Molmil
RNA-nsp9 bound to the NiRAN domain of the E-RTC with an empty G-pocket
Descriptor: ADENOSINE MONOPHOSPHATE, Non-structural protein 9, RNA-directed RNA polymerase, ...
Authors:Small, G.I, Darst, S.A, Campbell, E.A.
Deposit date:2024-09-06
Release date:2025-03-19
Method:ELECTRON MICROSCOPY (2.58 Å)
Cite:Matters arising: There is no structure of the catalytic intermediate of GTP-mediated mRNA capping by the SARS-CoV-2 NiRAN domain, and thus the mechanism remains unknown
To Be Published
9EL4
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BU of 9el4 by Molmil
Crystal Structure of SARS-CoV-2 Mpro mutant E166A with Pfizer Intravenous Inhibitor PF-00835231
Descriptor: 3C-like proteinase nsp5, GLYCEROL, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zvornicanin, S.N, Shaqra, A.M, Schiffer, C.A.
Deposit date:2024-12-03
Release date:2025-03-19
Last modified:2025-05-21
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Molecular mechanisms of drug resistance and compensation in SARS-CoV-2 main protease: the interplay between E166 and L50.
Mbio, 16, 2025
9ELV
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BU of 9elv by Molmil
Crystal Structure of SARS-CoV-2 Mpro mutant E166V with Pfizer Intravenous Inhibitor PF-00835231
Descriptor: 3C-like proteinase nsp5, GLYCEROL, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Zvornicanin, S.N, Shaqra, A.M, Schiffer, C.A.
Deposit date:2024-12-05
Release date:2025-03-19
Last modified:2025-05-21
Method:X-RAY DIFFRACTION (1.62 Å)
Cite:Molecular mechanisms of drug resistance and compensation in SARS-CoV-2 main protease: the interplay between E166 and L50.
Mbio, 16, 2025
9L09
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BU of 9l09 by Molmil
SARS-CoV-2 C-RTC with 13-TP
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Huang, Y.C, Liang, L, Liu, Y.X, Yan, L.M, Lou, Z.Y, Rao, Z.H.
Deposit date:2024-12-12
Release date:2025-03-19
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Discovery of a 2'-a-Fluoro-2'-b-C-(fluoromethyl) Purine Nucleotide Prodrug as a Potential Oral Anti-SARS-CoV-2 Agent
J Med Chem, 68, 2025
9L6C
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BU of 9l6c by Molmil
Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Fab ConD-852, Heavy chain of Fab P2C-1F11, ...
Authors:Zheng, Z, Bing, J, Congcong, L, Bing, Z.
Deposit date:2024-12-24
Release date:2025-03-19
Method:ELECTRON MICROSCOPY (3.33 Å)
Cite:Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs
To Be Published
9MEI
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BU of 9mei by Molmil
Crystal Structure of SARS-CoV-2 Mpro mutant L50F E166V with Pfizer Intravenous Inhibitor PF-00835231
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Zvornicanin, S.N, Shaqra, A.M, Schiffer, C.A.
Deposit date:2024-12-06
Release date:2025-03-19
Last modified:2025-05-21
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Molecular mechanisms of drug resistance and compensation in SARS-CoV-2 main protease: the interplay between E166 and L50.
Mbio, 16, 2025

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