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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
8XEF
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BU of 8xef by Molmil
Cocktail GC2050-GC2225
Descriptor: GC2050 heavy chain, GC2050 light chain, GC2225 heavy chain, ...
Authors:Feng, L.L.
Deposit date:2023-12-11
Release date:2024-12-11
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (4.41 Å)
Cite:XBB.1.5 RBD in complex with GC2050 and GC2225
To Be Published
9CJ6
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BU of 9cj6 by Molmil
Crystal Structure of SARS-CoV-2 N-NTD with part of N-arm complex with ssDNA.
Descriptor: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), Nucleoprotein
Authors:Maiti, A, Matsuo, H.
Deposit date:2024-07-05
Release date:2024-12-11
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Affinity Tag-Free Purification of SARS-CoV-2 N Protein and Its Crystal Structure in Complex with ssDNA.
Biomolecules, 14, 2024
8JAP
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BU of 8jap by Molmil
Cryo-EM structure of SARS-CoV-2 WT RBD in complex with W328-6H2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, H chain of W328-6H2 Fab region, L chain of W328-6H2 Fab region, ...
Authors:Nan, X.Y, Li, Y.J.
Deposit date:2023-05-06
Release date:2024-12-18
Method:ELECTRON MICROSCOPY (3.81 Å)
Cite:Cryo-EM structure of SARS-CoV-2 WT RBD in complex with W328-6H2 (local refinement)
To Be Published
8V5V
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BU of 8v5v by Molmil
Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open 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, Spike protein S2,Fibritin, ...
Authors:Olmedillas, E, Diaz, R, Hastie, K, Ollmann-Saphire, E.
Deposit date:2023-12-01
Release date:2024-12-18
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
To Be Published
8XRQ
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BU of 8xrq by Molmil
SARS-CoV-2 BA.1 spike RBD in complex bound with VacBB-639
Descriptor: Heavy chain of VacBB 639 Fab, Light chain of VacBB 639 Fab, Spike protein S1
Authors:Liu, C.C, Ju, B, Zhang, Z.
Deposit date:2024-01-08
Release date:2024-12-18
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (4.19 Å)
Cite:Rapid clonal expansion and somatic hypermutation contribute to the fate of SARS-CoV-2 broadly neutralizing antibodies.
J Immunol., 214, 2025
9BIH
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BU of 9bih by Molmil
SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA with 1 nucleotide bulge
Descriptor: RNA (34-mer), RNA (35-mer), Uridylate-specific endoribonuclease nsp15
Authors:Wright, Z.M, Butay, K.J, Krahn, J.M, Borgnia, M.J, Stanley, R.E.
Deposit date:2024-04-23
Release date:2024-12-18
Last modified:2025-01-15
Method:ELECTRON MICROSCOPY (3.24 Å)
Cite:Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates.
Nat Commun, 16, 2025
8ZPP
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BU of 8zpp by Molmil
Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab
Descriptor: Spike glycoprotein,Fibritin, variable heavy chain of ORB10 Fab, variable light chain of ORB10 Fab
Authors:Cao, S, Leng, C, Hu, H.
Deposit date:2024-05-30
Release date:2024-12-25
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab
To Be Published
9BF9
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BU of 9bf9 by Molmil
Human LAG-3-HLA-DR1 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, DI(HYDROXYETHYL)ETHER, HLA class II histocompatibility antigen DR beta chain, ...
Authors:Petersen, J, Rossjohn, J.
Deposit date:2024-04-17
Release date:2024-12-25
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:Crystal structure of the human LAG-3-HLA-DR1-peptide complex.
Sci Immunol, 9, 2024
8RJ5
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BU of 8rj5 by Molmil
P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex
Descriptor: Beta-2-microglobulin, MHC class I antigen, P1-15 T-cell Receptor Alpha Chain, ...
Authors:Wall, A, Sewell, A.K, Motozono, C, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-20
Release date:2025-01-01
Method:X-RAY DIFFRACTION (3.02 Å)
Cite:NF9 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex (Paper Pending)
To Be Published
8RJH
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BU of 8rjh by Molmil
HLA A*2402-NF9_6F pMHC complex
Descriptor: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE, Beta-2-microglobulin, MHC class I antigen
Authors:Wall, A, Sewell, A.K, Motozono, C, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-21
Release date:2025-01-01
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:HLA A*2402-NF9_6F pMHC complex
To Be Published
8RJI
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BU of 8rji by Molmil
HLA A*2402-NF9_5R pMHC complex
Descriptor: Beta-2-microglobulin, MHC class I antigen, Spike glycoprotein
Authors:Wall, A, Motozono, C, Sewell, A.K, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-21
Release date:2025-01-01
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:HLA A*2402-NF9_5R pMHC complex
To Be Published
8Y4D
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BU of 8y4d by Molmil
Crystal structure of SARS-Cov-2 main protease 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:2024-01-30
Release date:2025-01-08
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Crystal structure of SARS-Cov-2 main protease in complex with Bofutrelvir
To Be Published
8Y4G
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BU of 8y4g by Molmil
Crystal structure of SARS-Cov-2 main protease G15S 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:Zeng, P, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-01-30
Release date:2025-01-08
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (1.93 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
8Y4H
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BU of 8y4h by Molmil
Crystal structure of SARS-Cov-2 main protease K90R 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:Guo, L, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-01-30
Release date:2025-01-08
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (1.93 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
8YDP
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BU of 8ydp by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SARS-CoV-2 inhibiting peptide Ce9, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDQ
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BU of 8ydq by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with Ce149
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide Ce149, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDR
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BU of 8ydr by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce59
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 inhibiting peptide Ce59, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDS
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BU of 8yds by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike protein in complex with Ce59
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SARS-CoV-2 inhibiting peptide Ce59, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDT
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BU of 8ydt by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce41
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 inhibiting peptide Ce41, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDU
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BU of 8ydu by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDV
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BU of 8ydv by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDW
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BU of 8ydw by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, SODIUM ION, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDX
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BU of 8ydx by Molmil
Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.2 variant) in complex with CeSPIACE
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CeSPIACE, Spike glycoprotein
Authors:Suzuki, H, Nakamura, S, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:ELECTRON MICROSCOPY (4.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDZ
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BU of 8ydz by Molmil
Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CeSPIACE, Spike glycoprotein
Authors:Suzuki, H, Nakamura, S, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:ELECTRON MICROSCOPY (5.2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
9IUP
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BU of 9iup by Molmil
KP.3 RBD in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Feng, L.L.
Deposit date:2024-07-22
Release date:2025-01-15
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2.
Cell Discov, 10, 2024

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PDB entries from 2025-07-09

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