8HOZ

Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir

• PDB DOI: https://doi.org/10.2210/pdb8HOZ/pdb

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


• Deposited: 2022-12-11 Released: 2023-12-13 
• Deposition Author(s): Lin, M., Liu, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.258 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 

Starting Model: experimental

Literature

Crystal Structure of SARS-CoV-2 Omicron Main Protease (Mpro) in Complex with Nirmatrelvir

Lin, M., Liu, X.

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: fluorescence resonance energy transfer

Macromolecule Content

• Total Structure Weight: 34.37 kDa 
• Atom Count: 2,437 
• Modelled Residue Count: 306 
• 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4WI	B [auth A]	(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide C23 H34 F3 N5 O4 WDVIRQQKRMIXGS-XIFHJVQQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.258 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.667	α = 90
b = 63.546	β = 90
c = 104.671	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
AutoProcess	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Lin, M., Liu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	92169109

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary