9CJO | pdb_00009cjo

X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants

• PDB DOI: https://doi.org/10.2210/pdb9CJO/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-07-07 Released: 2025-07-09 
• Deposition Author(s): Esler, M.A., Shi, K., Harris, R.S., Aihara, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.273 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants

Esler, M.A., Shi, K., Harris, R.S., Aihara, H.

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)

Macromolecule Content 

• Total Structure Weight: 33.83 kDa 
• Atom Count: 2,337 
• Modeled Residue Count: 301 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 4  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: 2.33 Å
• R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.206	α = 90
b = 53.666	β = 101.55
c = 45.195	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Esler, M.A., Shi, K., Harris, R.S., Aihara, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA214279
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37 AI064064

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release