8XWT | pdb_00008xwt

Crystal structure of SARS-CoV-2 3CLpro-L50F mutant with its peptidyl substrate

• PDB DOI: https://doi.org/10.2210/pdb8XWT/pdb

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


• Deposited: 2024-01-16 Released: 2025-01-22 
• Deposition Author(s): Zhang, L.J., Hu, Q.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SARS-CoV-2 3CLpro-L50F mutant with its peptidyl substrate

Zhang, L.J., Hu, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.33 kDa 
• Atom Count: 2,664 
• Modeled Residue Count: 315 
• Deposited Residue Count: 320 
• Unique protein chains: 2

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): 2  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYS-SER-GLY-VAL-THR-PHE-GLN-SER-ALA-VAL-LYS-ARG-THR-ILE	B	14	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.57	α = 90
b = 81.222	β = 96.5
c = 87.056	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Zhang, L.J., Hu, Q.

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Funding Organization	Location	Grant Number
Other private	China	--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release