9JUF | pdb_00009juf

PEDV 3CLpro mutant (C144A) in complex with nsp9|10 peptidyl substrate

PDB DOI: https://doi.org/10.2210/pdb9JUF/pdb

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

Deposited: 2024-10-08 Released: 2025-10-22
Deposition Author(s): Zhang, Y., Liang, R., Shi, Y.J., Peng, G.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.198 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

PEDV 3CLpro mutant (C144A) in complex with nsp9|10 peptidyl substrate

Zhang, Y., Liang, R., Shi, Y.J., Peng, G.Q.

To be published.

Macromolecule Content

Total Structure Weight: 70.1 kDa
Atom Count: 4,937
Modeled Residue Count: 606
Deposited Residue Count: 640
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A023J7B5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	C, D	10	Porcine epidemic diarrhea virus	Mutation(s): 0
UniProt
Find proteins for P0C6V6 (Porcine epidemic diarrhea virus (strain CV777)) Explore P0C6V6 Go to UniProtKB: P0C6V6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C6V6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.198 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.001	α = 90
b = 91.096	β = 99.98
c = 57.944	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.