7XB4

Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with PF07321332

• PDB DOI: https://doi.org/10.2210/pdb7XB4/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-03-20 Released: 2023-03-22 
• Deposition Author(s): Hu, X.H., Li, J., Zhang, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.240 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Literature

Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with PF07321332

Hu, X.H., Li, J., Zhang, J.

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: 68.65 kDa 
• Atom Count: 4,514 
• Modelled Residue Count: 593 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1  Go to UniProtKB:  P0DTC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4WI (Subject of Investigation/LOI)	C [auth A], D [auth B]	(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: 2.07 Å
• R-Value Free: 0.240 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.152	α = 90
b = 102.656	β = 90
c = 103.355	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Hu, X.H., Li, J., Zhang, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description