› 4izj

X-ray diffraction
2.5Å resolution

Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme complexes and product complexes.

Released:
DOI: 10.2210/pdb4izj/pdb
PDB entry 4izj coloured by chain, front view.
PDB entry 4izj coloured by chain, side view.
PDB entry 4izj 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:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
PP Chains: A, E
Molecule details ›
Chains: A, E
Length: 210 amino acids
Theoretical weight: 22.34 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 Chains: B, C
Molecule details ›
Chains: B, C
Length: 210 amino acids
Theoretical weight: 22.33 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: D
Molecule details ›
Chain: D
Length: 210 amino acids
Theoretical weight: 22.33 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

3 bound ligands:
Ligand BME 6 x BME
Ligand MG 1 x MG
Ligand GOL 1 x GOL
1 modified residue:
Ligand CSO 7 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 41.61Å b: 64.33Å c: 187.74Å
α: 90° β: 95.8° γ: 90°
R-values:
R R work R free
0.182 0.178 0.244
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

1 mention without citation

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 et al. (2013)