8C9U

Crystal structure of SARS-CoV-2 Mpro-Q189K mutant in complex with nirmatrelvir

• PDB DOI: https://doi.org/10.2210/pdb8C9U/pdb

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


• Deposited: 2023-01-23 Released: 2024-08-07 
• Deposition Author(s): El Kilani, H., Hilgenfeld, R.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.210 
• R-Value Work: 0.188 

Starting Model: other

Literature

Crystal structure of SARS-CoV-2 Mpro-Q189K mutant in complex with nirmatrelvir

El Kilani, H., Hilgenfeld, R.

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: 34.2 kDa 
• Atom Count: 2,623 
• Modelled Residue Count: 305 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 11	A [auth AAA]	305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
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 AAA]	(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: 1.75 Å
• R-Value Free: 0.210 
• R-Value Work: 0.188 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.213	α = 90
b = 64.476	β = 90
c = 105.301	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): El Kilani, H., Hilgenfeld, R.

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Funding Organization	Location	Grant Number
European Commission	European Union	--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release
  
• Version 2.0: 2024-09-18
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-06
  Changes: Structure summary