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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 "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. Finally, the "New entries" tab contains the latest entries released this week.

Created: 2020-03-11 (last edited: 4 weeks ago)2020-07-17
Repr. entries (123)All entries (317)New entries (5)
7JIW
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THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 IN COMPLEX WITH PLP_SNYDER530
Descriptor:Papain-Like Protease, 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ZINC ION, ...
Authors:Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-07-23
Release date:2020-08-05
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530
to be published
7JIR
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THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 , C111S MUTANT, IN COMPLEX WITH PLP_SNYDER457
Descriptor:Papain-like protease, 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide, ZINC ION, ...
Authors:Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-07-23
Release date:2020-08-05
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder457
to be published
7JIV
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THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 , C111S MUTANT, IN COMPLEX WITH PLP_SNYDER530
Descriptor:Papain-like protease, 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ZINC ION, ...
Authors:Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-07-23
Release date:2020-08-05
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder530
to be published
7JIT
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THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 , C111S MUTANT, IN COMPLEX WITH PLP_SNYDER495
Descriptor:Papain-like protease, 5-[(carbamoylcarbamoyl)amino]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ZINC ION, ...
Authors:Osipiuk, J., Tesar, C., Endres, M., Lisnyak, V., Maki, S., Taylor, C., Zhang, Y., Zhou, Z., Azizi, S.A., Jones, K., Kathayat, R., Snyder, S.A., Dickinson, B.C., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-07-23
Release date:2020-08-05
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder495
to be published
6WC1
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PEPTIDE-BOUND SARS-COV-2 NSP9 RNA-REPLICASE
Descriptor:SARS-coV-2 Non-structural protein 9, SULFATE ION
Authors:Littler, D.R., Gully, B.S., Rossjohn, J.
Deposit date:2020-03-28
Release date:2020-08-05
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Identification of a putative peptide-binding site at the dimer interface of the SARS-CoV-2 Nsp9 RNA-replicase.
To Be Published
6ZOK
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SARS-COV-2-NSP1-40S COMPLEX, FOCUSED ON BODY
Descriptor:18S ribosomal RNA, 40S ribosomal protein SA, 40S ribosomal protein S3a, ...
Authors:Schubert, K., Karousis, E.D., Jomaa, A., Scaiola, A., Echeverria, B., Gurzeler, L.-A., Leibundgut, M., Thiel, V., Muehlemann, O., Ban, N.
Deposit date:2020-07-07
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:SARS-CoV-2-Nsp1-40S, focused on body
To Be Published
6ZLW
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SARS-COV-2 NSP1 BOUND TO THE HUMAN 40S RIBOSOMAL SUBUNIT
Descriptor:40S ribosomal protein SA, 40S ribosomal protein S3a, 40S ribosomal protein S2, ...
Authors:Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.
Deposit date:2020-07-01
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (2.6 Å)
Cite:Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 2020
6ZSL
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CRYSTAL STRUCTURE OF THE SARS-COV-2 HELICASE AT 1.94 ANGSTROM RESOLUTION
Descriptor:SARS-CoV-2 helicase NSP13, ZINC ION, PHOSPHATE ION
Authors:Newman, J.A., Yosaatmadja, Y., Douangamath, A., Arrowsmith, C.H., von Delft, F., Edwards, A., Bountra, C., Gileadi, O.
Deposit date:2020-07-15
Release date:2020-07-29
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution
To Be Published
7C7P
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CRYSTAL STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE IN COMPLEX WITH TELAPREVIR
Descriptor:main protease, (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide, CHLORIDE ION, ...
Authors:Zeng, R., Qiao, J.X., Wang, Y.F., Li, Y.S., Yao, R., Yang, S.Y., Lei, J.
Deposit date:2020-05-26
Release date:2020-07-29
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir
To Be Published
6ZOW
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SARS-COV-2 SPIKE IN PREFUSION STATE
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Martinez, M., Marabini, R., Carazo, J.M.
Deposit date:2020-07-07
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.
Biorxiv, 2020
6ZP5
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SARS-COV-2 SPIKE IN PREFUSION STATE (FLEXIBILITY ANALYSIS, 1-UP CLOSED CONFORMATION)
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Martinez, M., Marabini, R., Carazo, J.M.
Deposit date:2020-07-08
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.
Biorxiv, 2020
6ZBP
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H11-H4 COMPLEX WITH SARS-COV-2
Descriptor:Spike glycoprotein, H11-H4, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Naismith, J.H., Huo, J., Mikolajek, H., Ward, P., Dumoux, M., Owens, R.J., LeBas, A.
Deposit date:2020-06-08
Release date:2020-07-29
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:H11-D4 complex with SARS-CoV-2 RBD
To Be Published
6ZDG
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ASSOCIATION OF THREE COMPLEXES OF LARGELY STRUCTURALLY DISORDERED SPIKE ECTODOMAIN WITH BOUND EY6A FAB
Descriptor:Spike glycoprotein, EY6A heavy chain, EY6A light chain, ...
Authors:Duyvesteyn, H.M.E., Zhou, D., Zhao, Y., Fry, E.E., Ren, J., Stuart, D.I.
Deposit date:2020-06-14
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (4.7 Å)
Cite:Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient
To Be Published
6XEZ
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STRUCTURE OF SARS-COV-2 REPLICATION-TRANSCRIPTION COMPLEX BOUND TO NSP13 HELICASE - NSP13(2)-RTC
Descriptor:nsp12, nsp8, nsp7, ...
Authors:Chen, J., Malone, B., Llewellyn, E.C., Campbell, E.A., Darst, S.A.
Deposit date:2020-06-14
Release date:2020-07-29
Last modified:2020-08-05
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.
Biorxiv, 2020
6XQB
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SARS-COV-2 RDRP/RNA COMPLEX
Descriptor:RNA-directed RNA polymerase, Non-structural protein 8, Non-structural protein 7, ...
Authors:Liu, B., Shi, W., Yang, Y.
Deposit date:2020-07-09
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structure of SARS-CoV-2 RdRp/RNA complex at 3.4 Angstroms resolution
To Be Published
6ZHD
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H11-H4 BOUND TO SPIKE
Descriptor:Spike glycoprotein,Fibritin, Nanobody H11-H4, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Clare, D.K., Naismith, J.H., Weckener, M., Vogirala, V.K.
Deposit date:2020-06-22
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:H11-H4 bound to Spike
To Be Published
7JFQ
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THE CRYSTAL STRUCTURE OF 3CL MAINPRO OF SARS-COV-2 WITH DE-OXIDIZED C145
Descriptor:3C-like proteinase, 1,2-ETHANEDIOL, FORMIC ACID
Authors:Tan, K., Maltseva, N.I., Welk, L.F., Jedrzejczak, R.P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2020-07-17
Release date:2020-07-29
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:The crystal structure of 3CL MainPro of SARS-CoV-2 with de-oxidized C145
To Be Published
6ZP7
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SARS-COV-2 SPIKE IN PREFUSION STATE (FLEXIBILITY ANALYSIS, 1-UP OPEN CONFORMATION)
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Martinez, M., Marabini, R., Carazo, J.M.
Deposit date:2020-07-08
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.
Biorxiv, 2020
6XM5
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STRUCTURE OF SARS-COV-2 SPIKE AT PH 5.5, ALL RBDS DOWN
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Zhou, T., Tsybovsky, Y., Olia, A., Kwong, P.D.
Deposit date:2020-06-29
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike.
Biorxiv, 2020
6ZON
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SARS-COV-2 NSP1 BOUND TO A HUMAN 43S PREINITIATION RIBOSOME COMPLEX - STATE 1
Descriptor:40S ribosomal protein SA, 40S ribosomal protein S3a, 40S ribosomal protein S2, ...
Authors:Thoms, M., Buschauer, R., Ameismeier, M., Denk, T., Kratzat, H., Mackens-Kiani, T., Cheng, J., Berninghausen, O., Becker, T., Beckmann, R.
Deposit date:2020-07-07
Release date:2020-07-29
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 2020
6ZP0
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STRUCTURE OF SARS-COV-2 SPIKE PROTEIN TRIMER (SINGLE ARG S1/S2 CLEAVAGE SITE) IN CLOSED STATE
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Xiong, X., Qu, K., Scheres, S.H.W., Briggs, J.A.G.
Deposit date:2020-07-08
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3 Å)
Cite:A thermostable, closed, SARS-CoV-2 spike protein trimer.
To Be Published
6XQT
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EXTREME MALLEABILITY OF THE SARS-COV-2 3CL MPRO ACTIVE SITE CAVITY FACILITATES BINDING OF CLINICAL ANTIVIRALS: PROSPECTS FOR REPURPOSING EXISTING DRUGS AND RAMIFICATIONS FOR INHIBITOR DESIGN
Descriptor:3C-like proteinase, (1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropyla mino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
Authors:Kneller, D.W., Kovalevsky, A., Coates, L.
Deposit date:2020-07-10
Release date:2020-07-22
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Extreme malleability of the SARS-CoV-2 3CL Mpro active site cavity facilitates binding of clinical antivirals: Prospects for repurposing existing drugs and ramifications for inhibitor design
To Be Published
6XQS
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EXTREME MALLEABILITY OF THE SARS-COV-2 3CL MPRO ACTIVE SITE CAVITY FACILITATES BINDING OF CLINICAL ANTIVIRALS: PROSPECTS FOR REPURPOSING EXISTING DRUGS AND RAMIFICATIONS FOR INHIBITOR DESIGN
Descriptor:3C-like proteinase, (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide
Authors:Kneller, D.W., Kovalevsky, A., Coates, L.
Deposit date:2020-07-10
Release date:2020-07-22
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Extreme malleability of the SARS-CoV-2 3CL Mpro active site cavity facilitates binding of clinical antivirals: Prospects for repurposing existing drugs and ramifications for inhibitor design
To Be Published
6ZP2
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STRUCTURE OF SARS-COV-2 SPIKE PROTEIN TRIMER (K986P, V987P, SINGLE ARG S1/S2 CLEAVAGE SITE) IN LOCKED STATE
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Xiong, X., Qu, K., Scheres, S.H.W., Briggs, J.A.G.
Deposit date:2020-07-08
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:A thermostable, closed, SARS-CoV-2 spike protein trimer.
To Be Published
6ZOX
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STRUCTURE OF DISULPHIDE-STABILIZED SARS-COV-2 SPIKE PROTEIN TRIMER (X2 DISULPHIDE-BOND MUTANT, G413C, V987C, SINGLE ARG S1/S2 CLEAVAGE SITE)
Descriptor:Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:Xiong, X., Qu, K., Scheres, S.H.W., Briggs, J.A.G.
Deposit date:2020-07-08
Release date:2020-07-22
Last modified:2020-07-29
Method:ELECTRON MICROSCOPY (3 Å)
Cite:A thermostable, closed, SARS-CoV-2 spike protein trimer.
To Be Published
167327
PDB entries from 2020-08-05