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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 (4510)Repr. entries (2011)Latest entries (2)
8UPX
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BU of 8upx by Molmil
Omicron-S-MERS-RBD
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,SARS-CoV-2 omicron spike with MERS RBD
Authors:Bu, F, Li, F, Liu, B.
Deposit date:2023-10-23
Release date:2024-08-21
Last modified:2024-09-11
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Pan-beta-coronavirus subunit vaccine prevents SARS-CoV-2 Omicron, SARS-CoV, and MERS-CoV challenge.
J.Virol., 2024
8YE4
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The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF
Descriptor: Beta-2-microglobulin, MHC class I antigen precusor, Spike protein S1, ...
Authors:Deng, S.S, Jin, T.C, Xu, Z.H, Wang, M.H.
Deposit date:2024-02-21
Release date:2024-08-21
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.
J.Biol.Chem., 300, 2024
8ZHD
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BU of 8zhd by Molmil
SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-26 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-10
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (3.41 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHE
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BU of 8zhe by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-26 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-10
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (3.16 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHF
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SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-26 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-10
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (5.26 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHG
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BU of 8zhg by Molmil
SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, focused refinement of RBD-Fab region
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-26 Fab, Light chain of R1-26 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-10
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (3.51 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHH
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BU of 8zhh by Molmil
SARS-CoV-2 spike trimer (6P) in complex with two H18 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-10
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (5.55 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHI
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BU of 8zhi by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-11
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (6.05 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHJ
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BU of 8zhj by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-11
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (8.45 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHK
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BU of 8zhk by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C3 symmetry)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-11
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (6.3 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHL
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BU of 8zhl by Molmil
SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-32 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-11
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (3.96 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHM
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BU of 8zhm by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-11
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (3.39 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHN
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BU of 8zhn by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs (one RBD rotated)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-11
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (4.12 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHO
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BU of 8zho by Molmil
SARS-CoV-2 S1 in complex with H18 and R1-32 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, Heavy chain of R1-32 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-11
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (3.54 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHP
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BU of 8zhp by Molmil
Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, Heavy chain of R1-32 Fab, ...
Authors:Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
Deposit date:2024-05-11
Release date:2024-08-21
Method:ELECTRON MICROSCOPY (3.66 Å)
Cite:Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZV9
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BU of 8zv9 by Molmil
Complex structure of HLA2402 with recognizing SARS-CoV-2 Y453F epitope NYNYLFRLF
Descriptor: 1,2-ETHANEDIOL, Beta-2-microglobulin, MHC class I antigen, ...
Authors:Deng, S.S, Jin, T.C, Xu, Z.H, Wang, M.H.
Deposit date:2024-06-11
Release date:2024-08-21
Last modified:2024-08-28
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.
J.Biol.Chem., 300, 2024
9F9Y
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BU of 9f9y by Molmil
SARS-CoV-2 BA-2.87.1 Spike ectodomain
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,Fibritin
Authors:Ren, J, Stuart, D.I, Duyvesteyn, H.M.E.
Deposit date:2024-05-09
Release date:2024-08-21
Last modified:2024-09-04
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike.
Structure, 2024
8TY3
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BU of 8ty3 by Molmil
MI-31 ligand bound to SARS-CoV-2 Mpro
Descriptor: (1S,3aR,6aS)-2-[(3,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}octahydrocyclopenta[c]pyrrole-1-carboxamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2023-08-24
Release date:2024-08-28
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:MI-31 bound to SARS-CoV-2 Mpro
To Be Published
8TY4
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BU of 8ty4 by Molmil
MI-30 bound to Mpro of SARS-CoV-2
Descriptor: (1S,3aR,6aS)-2-[(2,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}octahydrocyclopenta[c]pyrrole-1-carboxamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2023-08-24
Release date:2024-08-28
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:MI-30 bound to SARS-CoV-2 Mpro
To Be Published
8TY5
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MI-14 bound to Mpro of SARS-CoV-2
Descriptor: (1R,2S,5S)-3-[(2,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2023-08-24
Release date:2024-08-28
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:MI-14 bound to SARS-CoV-2 Mpro
To Be Published
8UG9
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XBB.1.5 spike/Nb5 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-5, ...
Authors:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2023-10-05
Release date:2024-08-28
Method:ELECTRON MICROSCOPY (3.49 Å)
Cite:XBB.1.5 spike/Nb5 complex
To Be Published
8WTI
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BU of 8wti by Molmil
Crystal structure of the SARS-CoV-2 main protease in complex with 20j
Descriptor: 3C-like proteinase nsp5, DI(HYDROXYETHYL)ETHER, SULFATE ION, ...
Authors:Zeng, R, Zhao, X, Yang, S.Y, Lei, J.
Deposit date:2023-10-18
Release date:2024-08-28
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Discovery of alpha-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups.
Bioorg.Chem., 143, 2024
9FEH
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BU of 9feh by Molmil
Crystal structure of SARS-CoV-2 nsp14 methyltransferase domain in complex with the STM957 inhibitor
Descriptor: Transcription factor ETV6,Guanine-N7 methyltransferase nsp14, ZINC ION, ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-5-(2-pyridin-3-ylethynyl)pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-3-cyano-~{N}-ethyl-4-methoxy-benzenesulfonamide
Authors:Zilecka, E, Klima, M, Boura, E.
Deposit date:2024-05-20
Release date:2024-08-28
Last modified:2024-09-04
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:Structure of SARS-CoV-2 MTase nsp14 with the inhibitor STM957 reveals inhibition mechanism that is shared with a poxviral MTase VP39.
J Struct Biol X, 10, 2024
9FQ9
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Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor PSB-21110 (compound 29b in publication)
Descriptor: (5-chloranylpyridin-3-yl) 4-ethoxy-2-fluoranyl-benzoate, BROMIDE ION, Non-structural protein 11
Authors:Strater, N, Claff, T, Sylvester, K, Oneto, A, Guetschow, M, Mueller, C.E.
Deposit date:2024-06-19
Release date:2024-08-28
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Nonpeptidic Irreversible Inhibitors of SARS-CoV-2 Main Protease with Potent Antiviral Activity.
J.Med.Chem., 2024
9FQA
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Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor PSB-21101 (compound 30b in publication)
Descriptor: (5-chloranylpyridin-3-yl) 2-fluoranyl-4-phenylmethoxy-benzoate, BROMIDE ION, MAGNESIUM ION, ...
Authors:Strater, N, Claff, T, Sylvester, K, Oneto, A, Guetschow, M, Mueller, C.E.
Deposit date:2024-06-14
Release date:2024-08-28
Method:X-RAY DIFFRACTION (1.47 Å)
Cite:Nonpeptidic Irreversible Inhibitors of SARS-CoV-2 Main Protease with Potent Antiviral Activity.
J.Med.Chem., 2024

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PDB entries from 2024-09-11

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