7C2Q

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 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

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 of Related Structures:  
  7C2Q

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Organizational Affiliation: 

The Second Affiliated Hospital of Nanchang University, Nanchang, 330031, China.

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 
• Modelled 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 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• 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