8CAC

Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K

• PDB DOI: https://doi.org/10.2210/pdb8CAC/pdb

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


• Deposited: 2023-01-24 Released: 2024-08-07 
• Deposition Author(s): Ibrahim, M., El Kilani, H., Hilgenfeld, R.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.272 
• R-Value Work: 0.212 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K

Ibrahim, M., 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: 67.98 kDa 
• Atom Count: 4,883 
• Modelled Residue Count: 603 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A [auth AAA], B [auth BBB]	302	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  EC: 3.4.22.69
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O6K (Subject of Investigation/LOI)	C [auth AAA], D [auth BBB]	~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate C31 H41 N5 O7 FRACPXUHUTXLCX-BELIEFIBSA-N
CL (Subject of Investigation/LOI)	E [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.272 
• R-Value Work: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.032	α = 90
b = 101.709	β = 90
c = 103.205	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Ibrahim, M., 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 1.1: 2024-10-09
  Changes: Structure summary