› 4izk

X-ray diffraction
2.3Å resolution

Crystal structure of yellowtail ascites virus VP4 protease active site mutant (K674A) reveals both an acyl-enzyme complex and an empty active site

Released:
DOI: 10.2210/pdb4izk/pdb
PDB entry 4izk coloured by chain, front view.
PDB entry 4izk coloured by chain, side view.
PDB entry 4izk coloured by chain, top view.
Source organism: Yellowtail ascites virus - Y-6
Primary publication:
Crystal structures of yellowtail ascites virus VP4 protease: trapping an internal cleavage site trans acyl-enzyme complex in a native Ser/Lys dyad active site.
Chung IY, Paetzel M
J Biol Chem 288 13068-81 (2013)
PMID: 23511637

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161024 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
PP Chain: A
Molecule details ›
Chain: A
Length: 210 amino acids
Theoretical weight: 22.27 KDa
Source organism: Yellowtail ascites virus - Y-6
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P89521 (Residues: 508-716; Coverage: 22%)
Sequence domains: Birnavirus VP4 protein
Structure domains: Ribosomal Protein S5; domain 2
PP Chain: B
Molecule details ›
Chain: B
Length: 210 amino acids
Theoretical weight: 22.25 KDa
Source organism: Yellowtail ascites virus - Y-6
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P89521 (Residues: 508-716; Coverage: 22%)
Sequence domains: Birnavirus VP4 protein
Structure domains: Ribosomal Protein S5; domain 2

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand BME 1 x BME
1 modified residue:
Ligand CSO 1 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: F4132
Unit cell:
a: 273.52Å b: 273.52Å c: 273.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.173 0.197
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.
Lee et al. (2020)
1 more

2 mentions without citation

The Stronger Downregulation of in vitro and in vivo Innate Antiviral Responses by a Very Virulent Strain of Infectious Bursal Disease Virus (IBDV), Compared to a Classical Strain, Is Mediated, in Part, by the VP4 Protein.
Dulwich et al. (2020)
1 more