7C2Y | pdb_00007c2y

The crystal structure of COVID-2019 main protease in the apo state

• PDB DOI: https://doi.org/10.2210/pdb7C2Y/pdb

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


• Deposited: 2020-05-10 Released: 2020-09-02 
• Deposition Author(s): Zhou, X.L., Zhong, F.L., Lin, C., Zhou, H., Hu, X.H., Wang, Q.S., Li, J., Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

COVID-2019 main protease in the apo state

Zhou, X.L., Zhong, F.L., Lin, C., Zhou, H., Hu, X.H., Wang, Q.S., Li, J., Zhang, J.

To be published.

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: 65.95 kDa 
• Atom Count: 4,383 
• Modeled Residue Count: 572 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	298	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: 1.91 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.88	α = 90
b = 102.34	β = 90
c = 103.49	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., Zhou, H., Hu, X.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: 2023-11-29
  Changes: Data collection, Database references, Refinement description