8R19 | pdb_00008r19

SARS-CoV-2 Mpro (Omicron, P132H) free enzyme

• PDB DOI: https://doi.org/10.2210/pdb8R19/pdb

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


• Deposited: 2023-11-01 Released: 2023-11-29 
• Deposition Author(s): Ibrahim, M., Sun, X., Hilgenfeld, R.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.237 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study

Ibrahim, M., Sun, X., Martins de Oliveira, V., Liu, R., Clayton, J., El Kilani, H., Shen, J., Hilgenfeld, R.

(2024) Hlife 2: 419-433

• DOI: https://doi.org/10.1016/j.hlife.2024.06.003

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.87 kDa 
• Atom Count: 2,557 
• Modeled Residue Count: 305 
• 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): 1  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:  0.237 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.079	α = 90
b = 53.2	β = 100.317
c = 112.825	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Ibrahim, M., Sun, X., Hilgenfeld, R.

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Funding Organization	Location	Grant Number
Other government	Germany	--

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Database references, Structure summary