PDBe 1vas

X-ray diffraction
2.75Å resolution

ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION

Released:

Function and Biology Details

Reactions catalysed:
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. 
Cleaves the N-glycosidic bond between the 5'-pyrimidine residue in cyclobutadipyrimidine (in DNA) and the corresponding deoxy-D-ribose residue. 
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease V Chain: A
Molecule details ›
Chain: A
Length: 137 amino acids
Theoretical weight: 15.97 KDa
Source organism: Enterobacteria phage T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P04418 (Residues: 2-138; Coverage: 99%)
Structure domains: T4 endonuclease V
DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.96 KDa
Source organism: Synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.99 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P65
Unit cell:
a: 118.82Å b: 118.82Å c: 36.28Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.152 0.152 0.24
Expression systems:
  • Escherichia coli
  • Not provided