8INU

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant in Complex with Inhibitor nirmatrelvir

• PDB DOI: https://doi.org/10.2210/pdb8INU/pdb

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


• Deposited: 2023-03-10 Released: 2024-03-13 
• 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: 1.69 Å
• R-Value Free: 0.214 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Literature

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant

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: 34.36 kDa 
• Atom Count: 2,708 
• 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	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b
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 (Subject of Investigation/LOI)	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: 1.69 Å
• R-Value Free: 0.214 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.604	α = 90
b = 63.769	β = 90
c = 105.672	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
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: 2024-03-13
  Type: Initial release