8GPH

Crystal structure of protease 3C (C160A mutant) from Seneca Valley Virus

• PDB DOI: https://doi.org/10.2210/pdb8GPH/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Senecavirus A
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-08-26 Released: 2023-05-24 
• Deposition Author(s): Zhao, H.F., Zhang, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.193 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Crystal structure of protease 3C (C160A mutant) from Seneca Valley Virus

Zhao, H.F., Zhang, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 23.16 kDa 
• Atom Count: 1,818 
• Modelled Residue Count: 208 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase C3	A	211	Senecavirus A	Mutation(s): 1
UniProt
Find proteins for A0A1U9IRU2 (Senecavirus A) Explore A0A1U9IRU2  Go to UniProtKB:  A0A1U9IRU2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.193 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.253	α = 90
b = 69.441	β = 90
c = 75.705	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Zhao, H.F., Zhang, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31970152

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description