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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
7N4L
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BU of 7n4l by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2125.
Descriptor: Spike protein S1, WRAIR-2125 antibody Fab heavy chain, WRAIR-2125 antibody Fab light chain
Authors:Sankhala, R.S, Joyce, M.G.
Deposit date:2021-06-04
Release date:2021-11-10
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (3.601 Å)
Cite:Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations.
Nat.Immunol., 22, 2021
7N4M
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2151.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, WRAIR-2151 antibody Fab heavy chain, ...
Authors:Sankhala, R.S, Joyce, M.G.
Deposit date:2021-06-04
Release date:2021-11-10
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (3.79 Å)
Cite:Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations.
Nat.Immunol., 22, 2021
7BNV
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Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-300
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy Chain, Light Chain, ...
Authors:Hall, G, Cowan, R, Carr, M.
Deposit date:2021-01-22
Release date:2021-11-17
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses.
Front Immunol, 12, 2021
7DFG
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BU of 7dfg by Molmil
Structure of COVID-19 RNA-dependent RNA polymerase bound to favipiravir
Descriptor: 6-fluoro-3-oxo-4-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydropyrazine-2-carboxamide, MAGNESIUM ION, Non-structural protein 7, ...
Authors:Li, Z, Zhou, Z, Yu, X.
Deposit date:2020-11-08
Release date:2021-11-17
Last modified:2024-05-29
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
To Be Published
7DFH
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BU of 7dfh by Molmil
Structure of COVID-19 RNA-dependent RNA polymerase bound to ribavirin
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Li, Z, Zhou, Z, Yu, X.
Deposit date:2020-11-08
Release date:2021-11-17
Last modified:2024-05-29
Method:ELECTRON MICROSCOPY (2.97 Å)
Cite:Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
To Be Published
7E5S
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BU of 7e5s by Molmil
SARS-CoV-2 S trimer with four-antibody cocktail complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FC05 heavy chain, FC05 light chain, ...
Authors:Sun, Y, Wang, L, Wang, N, Feng, R, Wang, X.
Deposit date:2021-02-20
Release date:2021-11-17
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structure-based development of three- and four-antibody cocktails against SARS-CoV-2 via multiple mechanisms.
Cell Res., 31, 2021
7E9T
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BU of 7e9t by Molmil
Nanometer resolution in situ structure of SARS-CoV-2 post-fusion spike
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, ...
Authors:Zhu, Y, Tai, L, Zhu, G, Yin, G, Sun, F.
Deposit date:2021-03-05
Release date:2021-11-17
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (10.9 Å)
Cite:Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein.
Proc.Natl.Acad.Sci.USA, 118, 2021
7NP1
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Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-360
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Immunoblobulin light chain, Immunoglobulin gamma-1 heavy chain, ...
Authors:Hall, G, Cowan, R, Carr, M.
Deposit date:2021-02-26
Release date:2021-11-17
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses.
Front Immunol, 12, 2021
7SO9
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BU of 7so9 by Molmil
SARS-CoV-2 S B.1.617.2 delta variant + S2M11 + S2L20 Global Refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, S2L20 Fab heavy chain, S2L20 Fab light chain, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-29
Release date:2021-11-17
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (2.4 Å)
Cite:Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Science, 374, 2021
7SOA
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BU of 7soa by Molmil
SARS-CoV-2 S NTD B.1.617.2 delta variant + S2L20 Local Refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2L20 Fab heavy chain, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-29
Release date:2021-11-17
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Science, 374, 2021
7SOB
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BU of 7sob by Molmil
SARS-CoV-2 S B.1.617.1 kappa variant + S309 + S2L20 Global Refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, S2L20 Fab heavy chain, S2L20 Fab light chain, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-29
Release date:2021-11-17
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (2.4 Å)
Cite:Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Science, 374, 2021
7SOC
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BU of 7soc by Molmil
SARS-CoV-2 S RBD B.1.617.1 kappa variant S309 Local Refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, S309 Fab heavy chain, S309 Fab light chain, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-29
Release date:2021-11-17
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Science, 374, 2021
7SOD
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BU of 7sod by Molmil
SARS-CoV-2 S NTD B.1.617.1 kappa variant S2L20 Local Refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2L20 Fab heavy chain, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-29
Release date:2021-11-17
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Science, 374, 2021
7SOE
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BU of 7soe by Molmil
SARS-CoV-2 S B.1.617.1 kappa variant + S2X303 Global Refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2X303 Fab heavy chain, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-29
Release date:2021-11-17
Last modified:2022-06-08
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Science, 374, 2021
7SOF
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BU of 7sof by Molmil
SARS-CoV-2 S NTD B.1.617.1 kappa variant S2X303 Local Refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, S2X303 Fab heavy chain, S2X303 Fab light chain, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-10-29
Release date:2021-11-17
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Science, 374, 2021
6X45
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BU of 6x45 by Molmil
SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)
Descriptor: Spike protein S2'
Authors:Kreitler, D.F, Outlaw, V.K, Gellman, S.H.
Deposit date:2020-05-22
Release date:2021-11-24
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Engineered peptides potently block entry of SARS-CoV-2 into human airway cells
To Be Published
7EFP
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BU of 7efp by Molmil
Structure of SARS-CoV-2 spike receptor-binding domain in complex with high affinity ACE2 mutant (S19W,N330Y)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Lu, G.W, Ye, F, Lin, X.
Deposit date:2021-03-22
Release date:2021-11-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.698 Å)
Cite:S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis.
Signal Transduct Target Ther, 6, 2021
7EFR
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BU of 7efr by Molmil
Structure of SARS-CoV-2 spike receptor-binding domain in complex with high affinity ACE2 mutant (T27W,N330Y)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Lu, G.W, Ye, F, Lin, X.
Deposit date:2021-03-23
Release date:2021-11-24
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.494 Å)
Cite:S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis.
Signal Transduct Target Ther, 6, 2021
7VNB
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BU of 7vnb by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with a human single domain antibody n3113
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, n3113
Authors:Yang, Z, Wang, Y, Kong, Y, Jin, Y, Wu, Y, Ying, T.
Deposit date:2021-10-10
Release date:2021-11-24
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.27 Å)
Cite:A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants.
Signal Transduct Target Ther, 6, 2021
7VND
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BU of 7vnd by Molmil
Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain antibody n3113 (UUD-state, 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, Spike glycoprotein, ...
Authors:Yang, Z, Wang, Y, Kong, Y, Jin, Y, Wu, Y, Ying, T.
Deposit date:2021-10-10
Release date:2021-11-24
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants.
Signal Transduct Target Ther, 6, 2021
7VNE
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BU of 7vne by Molmil
Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain antibody n3113.1 (UUU-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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Yang, Z, Wang, Y, Kong, Y, Jin, Y, Wu, Y, Ying, T.
Deposit date:2021-10-10
Release date:2021-11-24
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants.
Signal Transduct Target Ther, 6, 2021
7VX1
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BU of 7vx1 by Molmil
SARS-CoV-2 Beta variant spike protein in open state
Descriptor: Spike glycoprotein
Authors:Xu, C, Cong, Y.
Deposit date:2021-11-12
Release date:2021-11-24
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7VX9
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BU of 7vx9 by Molmil
SARS-CoV-2 Kappa variant spike protein in complex wth ACE2, state C1
Descriptor: Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Xu, C, Cong, Y.
Deposit date:2021-11-12
Release date:2021-11-24
Last modified:2022-03-16
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7B0B
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BU of 7b0b by Molmil
Fab HbnC3t1p1_C6 bound to SARS-CoV-2 RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab heavy chain, IGK@ protein, ...
Authors:Borenstein-Katz, A, Diskin, R.
Deposit date:2020-11-19
Release date:2021-12-01
Last modified:2024-10-16
Method:X-RAY DIFFRACTION (2.98 Å)
Cite:Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants.
Immunity, 56, 2023
7DG6
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BU of 7dg6 by Molmil
Structure of SARS-Cov2-Mpro-1-302
Descriptor: Replicase polyprotein 1ab
Authors:Fu, Z, Liu, M, Huang, H.
Deposit date:2020-11-11
Release date:2021-12-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structure of SARS-CoV-2-Mpro-1-302
To Be Published

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