7C2Q | pdb_00007c2q

The crystal structure of COVID-19 main protease in the apo state

• PDB DOI: https://doi.org/10.2210/pdb7C2Q/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-08 Released: 2020-09-02 
• Deposition Author(s): Zhou, X.L., Zhong, F.L., Lin, C., Hu, X.H., Zhou, H., Wang, Q.S., Li, j., Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Structure of SARS-CoV-2 main protease in the apo state.

Zhou, X., Zhong, F., Lin, C., Hu, X., Zhang, Y., Xiong, B., Yin, X., Fu, J., He, W., Duan, J., Fu, Y., Zhou, H., McCormick, P.J., Wang, Q., Li, J., Zhang, J.

(2021) Sci China Life Sci 64: 656-659

• PubMed: 32880863 
• DOI: https://doi.org/10.1007/s11427-020-1791-3
• Primary Citation Related Structures: 
  7C2Q

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Organizational Affiliation: 
• School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China.
Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, 518118, China.
Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou, 341000, China.
The Second Affiliated Hospital of Nanchang University, Nanchang, 330031, China.
Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang, 110142, China.
Biotech & Biomedicine Science (Jiangxi) Co. Ltd, Ganzhou, 341000, China.
Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, 330047, China.
Human Aging Research Institute (HARI), School of Life Sciences, Nanchang University, Nanchang, 330031, China.
School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China.
Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary, University of London, London, EC1M 6BQ, UK.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China. [e-mail].
College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China. [e-mail].
Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, 341000, China. [e-mail].
School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.66 kDa 
• Atom Count: 4,467 
• Modeled Residue Count: 572 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	296	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.95	α = 90
b = 102.66	β = 90
c = 103.54	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-02 
Deposition Author(s): Zhou, X.L., Zhong, F.L., Lin, C., Hu, X.H., Zhou, H., Wang, Q.S., Li, j., Zhang, J.

Revision History  

• Version 1.0: 2020-09-02
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Structure summary
• Version 1.2: 2021-04-28
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Database references, Refinement description