5ZQG | pdb_00005zqg

Complex structure of PEDV 3CLpro mutant (C144A) with NEMO-231 peptite substrate

• PDB DOI: https://doi.org/10.2210/pdb5ZQG/pdb

• Classification: HYDROLASE/PEPTIDE
• Organism(s): Porcine epidemic diarrhea virus, Sus scrofa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-04-18 Released: 2019-05-22 
• Deposition Author(s): Gang, Y., Chen, J.Y., Dang, W., Xiao, S.B., Peng, G.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Complex structure of PEDV 3CLpro mutant (C144A) with NEMO peptite substrate

Gang, Y., Chen, J.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local 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: 68.57 kDa 
• Atom Count: 4,880 
• Modeled Residue Count: 593 
• Deposited Residue Count: 627 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein	A, B	308	Porcine epidemic diarrhea virus	Mutation(s): 1
UniProt
Find proteins for R4JK63 (Porcine epidemic diarrhea virus) Explore R4JK63  Go to UniProtKB:  R4JK63

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE LEU-ALA-GLN-LEU-GLN-VAL-ALA	C	11	Sus scrofa	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.576	α = 90
b = 92.434	β = 100.21
c = 58.029	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Gang, Y., Chen, J.Y., Dang, W., Xiao, S.B., Peng, G.Q.

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description