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: 2020-03-11 (last edited: yesterday)2020-10-28
All entries (509)Repr. entries (215)Latest entries (9)
7JJC
  • Download 7jjc
  • View 7jjc
Molmil generated image of 7jjc
CRYSTAL STRUCTURE OF NEUROPILIN-1 B1 DOMAIN IN COMPLEX WITH SARS-COV-2 S1 C-END RULE (CENDR) PEPTIDE
Descriptor:Neuropilin-1, Spike glycoprotein, DI(HYDROXYETHYL)ETHER, ...
Authors:Chen, K.-E., Collins, B.M.
Deposit date:2020-07-25
Release date:2020-10-28
Method:X-RAY DIFFRACTION (2.36 Å)
Cite:Neuropilin-1 is a host factor for SARS-CoV-2 infection
Science, 2020
7K9Z
  • Download 7k9z
  • View 7k9z
Molmil generated image of 7k9z
CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX WITH THE FAB FRAGMENTS OF NEUTRALIZING ANTIBODIES 298 AND 52
Descriptor:52 Fab Heavy Chain, 52 Fab Light Chain, 298 Fab Light Chain, ...
Authors:Newton, J.C., Kucharska, I., Rujas, E., Cui, H., Julien, J.P.
Deposit date:2020-09-29
Release date:2020-10-28
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers
Biorxiv, 2020
7D1M
  • Download 7d1m
  • View 7d1m
Molmil generated image of 7d1m
CRYSTAL STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE COMPLEXED WITH GC376
Descriptor:3C-like proteinase, (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, DIMETHYL SULFOXIDE
Authors:Fu, L.F., Gilski, M., Shabalin, I., Gao, G.F., Qi, J.X.
Deposit date:2020-09-14
Release date:2020-10-28
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:CRYSTAL STRUCTURE OF THE SARS-CoV-2 MAIN PROTEASE COMPLEXED WITH GC376
To Be Published
7KFI
  • Download 7kfi
  • View 7kfi
Molmil generated image of 7kfi
SARS-COV-2 MAIN PROTEASE IMMATURE FORM - APO STRUCTURE
Descriptor:Main protease, DIMETHYL SULFOXIDE, DI(HYDROXYETHYL)ETHER
Authors:Noske, G.D., Nakamura, A.M., Gawriljuk, V.O., Lima, G.A.M., Zeri, A.C.M., Nascimento, A.F.Z., Oliva, G., Godoy, A.S.
Deposit date:2020-10-14
Release date:2020-10-28
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:SARS-CoV-2 Main protease immature form - apo structure
To Be Published
7KG3
  • Download 7kg3
  • View 7kg3
Molmil generated image of 7kg3
CRYSTAL STRUCTURE OF COV-2 NSP3 MACRODOMAIN
Descriptor:Non-structural protein 3, MALONATE ION, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Arvai, A., Brosey, C.A., Link, T., Jones, D.E., Ahmed, Z., Tainer, J.A.
Deposit date:2020-10-15
Release date:2020-10-28
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors
To Be Published
7ACT
  • Download 7act
  • View 7act
Molmil generated image of 7act
THE SARS-COV-2 NUCLEOCAPSID PHOSPHOPROTEIN N-TERMINAL DOMAIN IN COMPLEX WITH 10MER SSRNA
Descriptor:Nucleoprotein, ssRNA
Authors:Veverka, V.
Deposit date:2020-09-11
Release date:2020-10-28
Method:SOLUTION NMR
Cite:The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 10mer ssRNA
To Be Published
7KFJ
  • Download 7kfj
  • View 7kfj
Molmil generated image of 7kfj
SARS-COV-2 MAIN PROTEASE IMMATURE FORM - FRAGMENT BBV-136614527
Descriptor:Main protease, DIMETHYL SULFOXIDE, DI(HYDROXYETHYL)ETHER, ...
Authors:Noske, G.D., Nakamura, A.M., Gawriljuk, V.O., Lima, G.A.M., Zeri, A.C.M., Nascimento, A.F.Z., Oliva, G., Godoy, A.S.
Deposit date:2020-10-14
Release date:2020-10-28
Method:X-RAY DIFFRACTION (2.66 Å)
Cite:SARS-CoV-2 Main protease immature form - fragment BBV-136614527
To Be Published
7AKU
  • Download 7aku
  • View 7aku
Molmil generated image of 7aku
STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO CALPEPTIN.
Descriptor:Replicase polyprotein 1ab, Calpeptin, CHLORIDE ION
Authors:Guenther, S., Reinke, P., Oberthuer, D., Yefanov, O., Gelisio, L., Ginn, H., Lieske, J., Domaracky, M., Brehm, W., Rahmani Mashour, A., White, T.A., Knoska, J., Pena Esperanza, G., Koua, F., Tolstikova, A., Groessler, M., Fischer, P., Hennicke, V., Fleckenstein, H., Trost, F., Galchenkova, M., Gevorkov, Y., Li, C., Awel, S., Paulraj, L.X., Ullah, N., Falke, S., Alves Franca, B., Schwinzer, M., Brognaro, H., Werner, N., Perbandt, M., Tidow, H., Seychell, B., Beck, T., Meier, S., Doyle, J.J., Giseler, H., Melo, D., Dunkel, I., Lane, T.J., Peck, A., Saouane, S., Hakanpaeae, J., Meyer, J., Noei, H., Gribbon, P., Ellinger, B., Kuzikov, M., Wolf, M., Zhang, L., Ehrt, C., Pletzer-Zelgert, J., Wollenhaupt, J., Feiler, C., Weiss, M., Schulz, E.C., Mehrabi, P., Norton-Baker, B., Schmidt, C., Lorenzen, K., Schubert, R., Han, H., Chari, A., Fernandez Garcia, Y., Turk, D., Hilgenfeld, R., Rarey, M., Zaliani, A., Chapman, H.N., Pearson, A., Betzel, C., Meents, A.
Deposit date:2020-10-02
Release date:2020-10-28
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structure of SARS-CoV-2 Main Protease bound to Calpeptin
To Be Published
7KHP
  • Download 7khp
  • View 7khp
Molmil generated image of 7khp
ACYL-ENZYME INTERMEDIATE STRUCTURE OF SARS-COV-2 MPRO IN COMPLEX WITH ITS C-TERMINAL AUTOPROCESSING SEQUENCE.
Descriptor:3C-like proteinase, DIMETHYL SULFOXIDE
Authors:Lee, J., Worrall, L.J., Paetzel, M., Strynadka, N.C.J.
Deposit date:2020-10-21
Release date:2020-10-28
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Crystallographic structure of wild-type SARS-CoV-2 Main Protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site
To Be Published
7K8M
  • Download 7k8m
  • View 7k8m
Molmil generated image of 7k8m
STRUCTURE OF THE SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C102
Descriptor:C102 Fab Heavy Chain, C102 Fab Light Chain, Surface glycoprotein, ...
Authors:Jette, C.A., Barnes, C.O., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Last modified:2020-10-28
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Nature, 2020
7K8Z
  • Download 7k8z
  • View 7k8z
Molmil generated image of 7k8z
STRUCTURE OF THE SARS-COV-2 S 2P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C135
Descriptor:Spike glycoprotein, C135 Fab Heavy Chain, C135 Fab Light Chain, ...
Authors:Barnes, C.O., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies
Nature, 2020
7KDT
  • Download 7kdt
  • View 7kdt
Molmil generated image of 7kdt
HUMAN TOM70 IN COMPLEX WITH SARS COV2 ORF9B
Descriptor:Mitochondrial import receptor subunit TOM70, ORF9b protein
Authors:QCRG Structural Biology Consortium
Deposit date:2020-10-09
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (3.05 Å)
Cite:Comparative Host-Coronavirus Protein Interaction Networks Reveal Pan-Viral Disease Mechanisms
Science, 2020
7K8V
  • Download 7k8v
  • View 7k8v
Molmil generated image of 7k8v
STRUCTURE OF THE SARS-COV-2 S 2P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C110
Descriptor:Spike glycoprotein, C110 Fab Heavy Chain, C110 Fab Light Chain, ...
Authors:Dam, K.A., Barnes, C.O., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Nature, 2020
7K8W
  • Download 7k8w
  • View 7k8w
Molmil generated image of 7k8w
STRUCTURE OF THE SARS-COV-2 S 2P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C119
Descriptor:Spike glycoprotein, C119 Fab Heavy Chain, C119 Fab Light Chain, ...
Authors:Sharaf, N.G., Barnes, C.O., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Nature, 2020
7K9P
  • Download 7k9p
  • View 7k9p
Molmil generated image of 7k9p
ROOM TEMPERATURE STRUCTURE OF NSP15 ENDORIBONUCLEASE FROM SARS COV-2 SOLVED USING SFX.
Descriptor:Uridylate-specific endoribonuclease, CITRIC ACID
Authors:Botha, S., Jernigan, R., Chen, J., Coleman, M.A., Frank, M., Grant, T.D., Hansen, D.T., Ketawala, G., Logeswaran, D., Martin-Garcia, J., Nagaratnam, N., Raj, A.L.L.X., Shelby, M., Yang, J.-H., Yung, M.C., Fromme, P.
Deposit date:2020-09-29
Release date:2020-10-21
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Room temperature structure of NendoU (Uridylate-specific endoribonuclease, Nsp15) solved using SFX.
To Be Published
7K8X
  • Download 7k8x
  • View 7k8x
Molmil generated image of 7k8x
STRUCTURE OF THE SARS-COV-2 S 2P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C121 (STATE 1)
Descriptor:Spike glycoprotein, C121 Fab Heavy chain, C121 Fab Light chain, ...
Authors:Abernathy, M.E., Barnes, C.O., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies
Nature, 2020
7K8S
  • Download 7k8s
  • View 7k8s
Molmil generated image of 7k8s
STRUCTURE OF THE SARS-COV-2 S 2P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C002 (STATE 1)
Descriptor:Spike glycoprotein, C002 Fab Heavy Chain, C002 Fab Light Chain, ...
Authors:Barnes, C.O., Malyutin, A.G., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Nature, 2020
7K8T
  • Download 7k8t
  • View 7k8t
Molmil generated image of 7k8t
STRUCTURE OF THE SARS-COV-2 S 6P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C002 (STATE 2)
Descriptor:Spike glycoprotein, C002 Fab Heavy Chain, C002 Fab Light Chain, ...
Authors:Malyutin, A.G., Barnes, C.O., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Last modified:2020-10-28
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Nature, 2020
7K90
  • Download 7k90
  • View 7k90
Molmil generated image of 7k90
STRUCTURE OF THE SARS-COV-2 S 6P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C144
Descriptor:Spike glycoprotein, C144 Fab Heavy Chain, C144 Fab Light Chain, ...
Authors:Barnes, C.O., Esswein, S.R., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (3.24 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.
Nature, 2020
7K8U
  • Download 7k8u
  • View 7k8u
Molmil generated image of 7k8u
STRUCTURE OF THE SARS-COV-2 S 6P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C104
Descriptor:Spike glycoprotein, C104 Fab Heavy Chain, C104 Fab Light Chain, ...
Authors:Barnes, C.O., Malyutin, A.G., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Last modified:2020-10-28
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies
Nature, 2020
7K8Y
  • Download 7k8y
  • View 7k8y
Molmil generated image of 7k8y
STRUCTURE OF THE SARS-COV-2 S 2P TRIMER IN COMPLEX WITH THE HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT, C121 (STATE 2)
Descriptor:Spike glycoprotein, C121 Fab Heavy chain, C121 Fab Light chain, ...
Authors:Abernathy, M.E., Barnes, C.O., Bjorkman, P.J.
Deposit date:2020-09-27
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (4.4 Å)
Cite:SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies
Nature, 2020
7A29
  • Download 7a29
  • View 7a29
Molmil generated image of 7a29
CRYO-EM STRUCTURE OF THE SARS-COV-2 SPIKE PROTEIN BOUND TO NEUTRALIZING SYBODIES (SB23) 2-UP CONFORMATION
Descriptor:Spike glycoprotein, Neutralising sybody (Sb23), 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Hallberg, B.M., Das, H.
Deposit date:2020-08-16
Release date:2020-10-21
Method:ELECTRON MICROSCOPY (2.94 Å)
Cite:Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2
BiorXiv, 2020
6ZPE
  • Download 6zpe
  • View 6zpe
Molmil generated image of 6zpe
NONSTRUCTURAL PROTEIN 10 (NSP10) FROM SARS COV-2
Descriptor:Replicase polyprotein 1ab, ZINC ION, GLYCEROL, ...
Authors:Fisher, S.Z., Kozielski, F.
Deposit date:2020-07-08
Release date:2020-10-14
Last modified:2020-10-21
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2.
Int J Mol Sci, 21, 2020
7JVA
  • Download 7jva
  • View 7jva
Molmil generated image of 7jva
SARS-COV-2 SPIKE IN COMPLEX WITH THE S2A4 NEUTRALIZING ANTIBODY FAB FRAGMENT (LOCAL REFINEMENT OF THE RECEPTOR-BINDING DOMAIN AND FAB VARIABLE DOMAINS)
Descriptor:S2A4 Fab heavy chain, S2A4 Fab light chain, SARS-CoV-2 spike glycoprotein, ...
Authors:Park, Y.J., Tortorici, M.A., Walls, A.C., Czudnochowski, N., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Snell, G., Veesler, D.
Deposit date:2020-08-20
Release date:2020-10-14
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
Cell(Cambridge,Mass.), 2020
7JVC
  • Download 7jvc
  • View 7jvc
Molmil generated image of 7jvc
SARS-COV-2 SPIKE IN COMPLEX WITH THE S2A4 NEUTRALIZING ANTIBODY FAB FRAGMENT
Descriptor:SARS-CoV-2 spike glycoprotein, S2A4 Fab heavy chain, S2A4 Fab light chain, ...
Authors:Park, Y.J., Tortorici, M.A., Walls, A.C., Czudnochowski, N., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Snell, G., Veesler, D.
Deposit date:2020-08-20
Release date:2020-10-14
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
Cell(Cambridge,Mass.), 2020
170383
PDB entries from 2020-10-28