9KZ3 | pdb_00009kz3

PEDV 3CLpro mutant (C144A) in complex with nsp8|9 peptite substrate

• PDB DOI: https://doi.org/10.2210/pdb9KZ3/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Porcine epidemic diarrhea virus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-12-09 Released: 2025-12-17 
• Deposition Author(s): Zhang, Y., Zhang, D., Zhang, Z.T., Shi, Y.J., Peng, G.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

PEDV 3CLpro mutant (C144A) in complex with nsp8|9 peptite substrate

Zhang, Y., Zhang, D., Zhang, Z.T., Shi, Y.J., Peng, G.Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 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)

Macromolecule Content 

• Total Structure Weight: 69.41 kDa 
• Atom Count: 4,859 
• Modeled Residue Count: 602 
• Deposited Residue Count: 632 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF1ab polyprotein	A, B	310	Porcine epidemic diarrhea virus	Mutation(s): 1
UniProt
Find proteins for A0A023J7B5 (Porcine epidemic diarrhea virus) Explore A0A023J7B5  Go to UniProtKB:  A0A023J7B5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	C	6	Porcine epidemic diarrhea virus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	D	6	Porcine epidemic diarrhea virus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.869	α = 90
b = 92.382	β = 100.07
c = 58.093	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Zhang, Y., Zhang, D., Zhang, Z.T., Shi, Y.J., Peng, G.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release