Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

COVID-19 featured content

This page is also available in: 日本語简体中文繁體中文한국어
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
8KEH
DownloadVisualize
BU of 8keh by Molmil
State 2 of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5
Descriptor: PW5-5 heavy chain, PW5-5 light chain, Spike glycoprotein
Authors:Sun, L, Mao, Q, Wang, Y.
Deposit date:2023-08-11
Release date:2024-09-04
Method:ELECTRON MICROSCOPY (3.21 Å)
Cite:Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8Y4C
DownloadVisualize
BU of 8y4c by Molmil
BA.2.86 S-trimer in complex with Nab XGv280
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, XGv280 Heavy chain, ...
Authors:Zhu, Q, Liu, P.
Deposit date:2024-01-30
Release date:2024-09-04
Method:ELECTRON MICROSCOPY (3.75 Å)
Cite:Enhancing RBD exposure and S1 shedding by an extremely conserved SARS-CoV-2 NTD epitope.
Signal Transduct Target Ther, 9, 2024
8YLS
DownloadVisualize
BU of 8yls by Molmil
Structure of SARS-CoV-2 Mpro in complex with its degrader
Descriptor: (4-methoxyphenyl)methyl ~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]pentan-2-yl]carbamate, 3C-like proteinase nsp5
Authors:Feng, Y, Li, W, Cheng, S.H, Li, X.B.
Deposit date:2024-03-06
Release date:2024-09-04
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:The Main Protease Degraders: Potent Broad-Spectrum Agents for Anti-Coronavirus Agents
To Be Published
8ZER
DownloadVisualize
BU of 8zer by Molmil
Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody P2C5, Spike protein S1, ...
Authors:Sluchanko, N.N, Varfolomeeva, L.A, Shcheblyakov, D.V, Logunov, D.Y, Gintsburg, A.L, Popov, V.O, Boyko, K.M.
Deposit date:2024-05-06
Release date:2024-09-04
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structural Basis for Evasion of New SARS-CoV-2 Variants from the Potent Virus-Neutralizing Nanobody Targeting the S-Protein Receptor-Binding Domain
Biochemistry Mosc.47, 89, 2024
8ZES
DownloadVisualize
BU of 8zes by Molmil
Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed with P2C5 nanobody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody P2C5, ...
Authors:Sluchanko, N.N, Varfolomeeva, L.A, Shcheblyakov, D.V, Logunov, D.Y, Gintsburg, A.L, Popov, V.O, Boyko, K.M.
Deposit date:2024-05-06
Release date:2024-09-04
Method:X-RAY DIFFRACTION (3.7 Å)
Cite:Structural Basis for Evasion of New SARS-CoV-2 Variants from the Potent Virus-Neutralizing Nanobody Targeting the S-Protein Receptor-Binding Domain
Biochemistry Mosc.47, 89, 2024
9EO6
DownloadVisualize
BU of 9eo6 by Molmil
SARS-CoV2 major protease in complex with a covalent inhibitor SLL11.
Descriptor: 3C-like proteinase nsp5, Inhibitor SLL11, POTASSIUM ION
Authors:Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
Deposit date:2024-03-14
Release date:2024-09-04
Last modified:2024-09-11
Method:X-RAY DIFFRACTION (2.11 Å)
Cite:Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 2024
9EOR
DownloadVisualize
BU of 9eor by Molmil
SARS-CoV2 major protease in complex with a covalent inhibitor SLL12.
Descriptor: 3C-like proteinase nsp5, Inhibitor SLL12, POTASSIUM ION
Authors:Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
Deposit date:2024-03-15
Release date:2024-09-04
Last modified:2024-09-11
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 2024
9EOX
DownloadVisualize
BU of 9eox by Molmil
SARS-CoV2 major protease in covalent complex with a soluble inhibitor.
Descriptor: 3C-like proteinase nsp5, POTASSIUM ION, Soluble inhibitor
Authors:Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
Deposit date:2024-03-15
Release date:2024-09-04
Last modified:2024-09-11
Method:X-RAY DIFFRACTION (2.54 Å)
Cite:Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 2024
8AJ1
DownloadVisualize
BU of 8aj1 by Molmil
SARS-CoV-2 Mpro in Complex with RK-107
Descriptor: (2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(phenylcarbamoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide, 3C-like proteinase nsp5
Authors:El Kilani, H, Hilgenfeld, R.
Deposit date:2022-07-27
Release date:2024-09-11
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:SARS-CoV-2 Mpro in Complex with RK-107
To Be Published
8Y4A
DownloadVisualize
BU of 8y4a by Molmil
BA.2.86 S-trimer in complex with Nab XG2v046
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:Zhu, Q, Liu, P.
Deposit date:2024-01-30
Release date:2024-09-11
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Enhancing RBD exposure and S1 shedding by an extremely conserved SARS-CoV-2 NTD epitope.
Signal Transduct Target Ther, 9, 2024

224931

PDB entries from 2024-09-11

PDB statisticsPDBj update infoContact PDBjnumon