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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:
242: Coronavirus Proteases

The "Representative PDB entries" tab contains only representative PDB entries with highest resolution, excluding the duplicate entries with 100% amino acid sequence identitiy, even if they contain a different ligand. The tab "All entries" contains all PDB IDs, in case you want to check all independent entries, including group depositions by same authors.

Created: 2020-03-11 (last edited: 2 days ago)2020-04-06
Representative PDB entries (23)All entries
6W9Q
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PEPTIDE-BOUND SARS-COV-2 NSP9 RNA-REPLICASE
Descriptor:SARS-CoV-2 3C-like proteinase peptide, Non-structural protein 9 fusion, PHOSPHATE ION
Authors:Littler, D.R., Gully, B.S., Riboldi-Tunnicliffe, A., Rossjohn, J.
Deposit date:2020-03-23
Release date:2020-04-08
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Identification of a putative peptide-binding site at the dimer interface of the SARS-CoV-2 Nsp9 RNA-replicase.
To Be Published
6W9C
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THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2
Descriptor:SARS-CoV-2 papain-like protease, ZINC ION, CHLORIDE ION
Authors:Osipiuk, J., Jedrzejczak, R., Tesar, C., Endres, M., Stols, L., Babnigg, G., Kim, Y., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-22
Release date:2020-04-01
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:The crystal structure of papain-like protease of SARS CoV-2
to be published
6M71
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SARS-COV-2 RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH COFACTORS
Descriptor:SARS-CoV-2 NSP12, SARS-CoV-2 NSP7, SARS-CoV-2 NSP8
Authors:Gao, Y., Yan, L., Huang, Y., Liu, F., Cao, L., Wang, T., Wang, Q., Lou, Z., Rao, Z.
Deposit date:2020-03-16
Release date:2020-04-01
Last modified:2020-04-08
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structure of 2019-nCoV RNA-dependent RNA polymerase in complex with cofactors at 2.9 Angstroms resolution.
To Be Published
6W6Y
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CRYSTAL STRUCTURE OF ADP RIBOSE PHOSPHATASE OF NSP3 FROM SARS COV-2 IN COMPLEX WITH AMP
Descriptor:SARS-CoV-2 ADP ribose phosphatase (ADRP), ADENOSINE MONOPHOSPHATE, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Authors:Michalska, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Mececar, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-18
Release date:2020-03-25
Last modified:2020-04-01
Method:X-RAY DIFFRACTION (1.451 Å)
Cite:Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in complex with AMP
To Be Published
6W41
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CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX WITH HUMAN ANTIBODY CR3022
Descriptor:CR3022 Fab heavy chain, CR3022 Fab light chain, Spike glycoprotein receptor binding domain, ...
Authors:Yuan, M., Wu, N.C., Zhu, X.Y., Wilson, I.A.
Deposit date:2020-03-09
Release date:2020-03-25
Last modified:2020-04-08
Method:X-RAY DIFFRACTION (3.084 Å)
Cite:A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV
Science, 2020
6YB7
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SARS-COV-2 MAIN PROTEASE WITH UNLIGANDED ACTIVE SITE (2019-NCOV, CORONAVIRUS DISEASE 2019, COVID-19)
Descriptor:SARS-CoV-2 main protease, DIMETHYL SULFOXIDE
Authors:Owen, C.D., Lukacik, P., Strain-Damerell, C.M., Douangamath, A., Powell, A.J., Fearon, D., Brandao-Neto, J., Crawshaw, A.D., Aragao, D., Williams, M., Flaig, R., Hall, D.R., McAuley, K.E., Mazzorana, M., Stuart, D.I., von Delft, F., Walsh, M.A.
Deposit date:2020-03-16
Release date:2020-03-25
Last modified:2020-04-08
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:COVID-19 main protease with unliganded active site
To Be Published
6W61
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CRYSTAL STRUCTURE OF THE METHYLTRANSFERASE-STIMULATORY FACTOR COMPLEX OF NSP16 AND NSP10 FROM SARS COV-2.
Descriptor:2'-O-methyltransferase NSP16, Stimulatory factor NSP10, CHLORIDE ION, ...
Authors:Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-15
Release date:2020-03-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2.
To Be Published
6LZG
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STRUCTURE OF NOVEL CORONAVIRUS SPIKE RECEPTOR-BINDING DOMAIN COMPLEXED WITH ITS RECEPTOR ACE2
Descriptor:Angiotensin-converting enzyme 2, SARS-CoV-2 Spike receptor-binding domain, N-ACETYL-D-GLUCOSAMINE, ...
Authors:Wang, Q.H., Song, H., Qi, J.X.
Deposit date:2020-02-19
Release date:2020-03-18
Last modified:2020-04-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2
To Be Published
6W4B
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THE CRYSTAL STRUCTURE OF NSP9 RNA BINDING PROTEIN OF SARS COV-2
Descriptor:Nsp9 replicase protein
Authors:Tan, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-10
Release date:2020-03-18
Last modified:2020-03-25
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:The crystal structure of Nsp9 replicase protein of COVID-19
To Be Published
6M0J
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CRYSTAL STRUCTURE OF SARS-COV-2 SPIKE RECEPTOR-BINDING DOMAIN BOUND WITH ACE2
Descriptor:Angiotensin-converting enzyme 2, SARS-CoV-2 receptor-binding domain, ZINC ION, ...
Authors:Wang, X., Lan, J., Ge, J., Yu, J., Shan, S.
Deposit date:2020-02-21
Release date:2020-03-18
Last modified:2020-04-08
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
Nature, 2020
6W4H
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1.80 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF NSP16 - NSP10 COMPLEX FROM SARS-COV-2
Descriptor:SARS-CoV-2 NSP16, SARS-CoV-2 NSP10, SULFITE ION, ...
Authors:Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Wiersum, G., Godzik, A., Jaroszewski, L., Stogios, P.J., Skarina, T., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-03-10
Release date:2020-03-18
Last modified:2020-04-01
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2
To Be Published
6M3M
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CRYSTAL STRUCTURE OF SARS-COV-2 NUCLEOCAPSID PROTEIN N-TERMINAL RNA BINDING DOMAIN
Descriptor:SARS-CoV-2 nucleocapsid protein
Authors:Chen, S., Kang, S.
Deposit date:2020-03-04
Release date:2020-03-18
Last modified:2020-04-08
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural insights of SARS-CoV-2 nucleocapsid protein RNA binding domain reveal potential unique drug targeting sites
To Be Published
6W02
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CRYSTAL STRUCTURE OF ADP RIBOSE PHOSPHATASE OF NSP3 FROM SARS COV-2 IN THE COMPLEX WITH ADP RIBOSE
Descriptor:ADP ribose phosphatase, ADENOSINE-5-DIPHOSPHORIBOSE, 1,2-ETHANEDIOL
Authors:Michalska, K., Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Mececar, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-02-28
Release date:2020-03-11
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose
To Be Published
6VYO
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CRYSTAL STRUCTURE OF RNA BINDING DOMAIN OF NUCLEOCAPSID PHOSPHOPROTEIN FROM SARS CORONAVIRUS 2
Descriptor:RNA binding domain of nucleocapsid protein, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, ...
Authors:Chang, C., Michalska, K., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Kim, Y., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-02-27
Release date:2020-03-11
Last modified:2020-04-08
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2
To Be Published
6VYB
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SARS-COV-2 SPIKE ECTODOMAIN STRUCTURE (OPEN STATE)
Descriptor:SARS-CoV-2 spike glycoprotein, N-ACETYL-D-GLUCOSAMINE
Authors:Walls, A.C., Park, Y.J., Tortorici, M.A., Wall, A., Seattle Structural Genomics Center for Infectious Disease (SSGCID), McGuire, A.T., Veesler, D.
Deposit date:2020-02-25
Release date:2020-03-11
Last modified:2020-04-01
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.
Cell, 2020
6M17
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THE 2019-NCOV RBD/ACE2-B0AT1 COMPLEX
Descriptor:Sodium-dependent neutral amino acid transporter B(0)AT1, Angiotensin-converting enzyme 2, SARS-coV-2 Receptor Binding Domain, ...
Authors:Yan, R.H., Zhang, Y.Y., Li, Y.N., Xia, L., Guo, Y.Y., Zhou, Q.
Deposit date:2020-02-24
Release date:2020-03-11
Last modified:2020-04-08
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
Science, 367, 2020
6W01
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THE 1.9 A CRYSTAL STRUCTURE OF NSP15 ENDORIBONUCLEASE FROM SARS COV-2 IN THE COMPLEX WITH A CITRATE
Descriptor:NSP15 Endoribonuclease, 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, ...
Authors:Kim, Y., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-02-28
Release date:2020-03-11
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate
To Be Published
6VXX
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STRUCTURE OF THE SARS-COV-2 SPIKE GLYCOPROTEIN (CLOSED STATE)
Descriptor:SARS-CoV-2 spike glycoprotein, N-ACETYL-D-GLUCOSAMINE
Authors:Walls, A.C., Park, Y.J., Tortorici, M.A., Wall, A., Seattle Structural Genomics Center for Infectious Disease (SSGCID), McGuire, A.T., Veesler, D.
Deposit date:2020-02-25
Release date:2020-03-11
Last modified:2020-04-01
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.
Cell, 2020
6VW1
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STRUCTURE OF 2019-NCOV CHIMERIC RECEPTOR-BINDING DOMAIN COMPLEXED WITH ITS RECEPTOR HUMAN ACE2
Descriptor:Angiotensin-converting enzyme 2, 2019-nCoV chimeric RBD, N-ACETYL-D-GLUCOSAMINE, ...
Authors:Shang, J., Ye, G., Shi, K., Wan, Y.S., Aihara, H., Li, F.
Deposit date:2020-02-18
Release date:2020-03-04
Last modified:2020-04-08
Method:X-RAY DIFFRACTION (2.68 Å)
Cite:Structural basis of receptor recognition by SARS-CoV-2
Nature, 2020
6LVN
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STRUCTURE OF THE 2019-NCOV HR2 DOMAIN
Descriptor:SARS-coV-2 S2 subunit
Authors:Zhu, Y., Sun, F.
Deposit date:2020-02-04
Release date:2020-02-26
Last modified:2020-04-01
Method:X-RAY DIFFRACTION (2.47 Å)
Cite:Crystal structure of HR2 domain of 2019-nCoV S2 subunit
To Be Published
6LXT
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STRUCTURE OF POST FUSION CORE OF 2019-NCOV S2 SUBUNIT
Descriptor:SARS-CoV-2 S2 subunit, TETRAETHYLENE GLYCOL, ZINC ION
Authors:Zhu, Y., Sun, F.
Deposit date:2020-02-11
Release date:2020-02-26
Last modified:2020-04-08
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion
Cell Res., 2020
6VSB
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PREFUSION 2019-NCOV SPIKE GLYCOPROTEIN WITH A SINGLE RECEPTOR-BINDING DOMAIN UP
Descriptor:SARS-CoV-2 spike glycoprotein, N-ACETYL-D-GLUCOSAMINE
Authors:Wrapp, D., Wang, N., Corbett, K.S., Goldsmith, J.A., Hsieh, C., Abiona, O., Graham, B.S., McLellan, J.S.
Deposit date:2020-02-10
Release date:2020-02-26
Last modified:2020-04-01
Method:ELECTRON MICROSCOPY (3.46 Å)
Cite:Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
Science, 367, 2020
6LU7
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THE CRYSTAL STRUCTURE OF COVID-19 MAIN PROTEASE IN COMPLEX WITH AN INHIBITOR N3
Descriptor:SARS-CoV-2 main protease, N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
Authors:Liu, X., Zhang, B., Jin, Z., Yang, H., Rao, Z.
Deposit date:2020-01-26
Release date:2020-02-05
Last modified:2020-03-18
Method:X-RAY DIFFRACTION (2.16 Å)
Cite:Structure of Mpro from COVID-19 virus and discovery of its inhibitors.
Biorxiv, 2020