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

X-ray diffraction
2.75Å resolution
PDB entry 1vas coloured by chain, front view.
PDB entry 1vas coloured by chain, side view.
PDB entry 1vas coloured by chain, top view.
Source organism: Tequatrovirus T4
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Endonuclease V and DNA
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Multimeric state: hetero trimer
Accessible surface area: 10367.6 Å2
Buried surface area: 3861.38 Å2
Dissociation area: 1,385.48 Å2
Dissociation energy (ΔGdiss): 7.65 kcal/mol
Dissociation entropy (TΔSdiss): 11.18 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-114719

Macromolecules

Endonuclease V
Chain: A
Length: 137 amino acids
Theoretical weight: 15.97 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P04418 (Residues: 2-138; Coverage: 99%)
Pfam: Pyrimidine dimer DNA glycosylase
InterPro:
CATH: T4 endonuclease V
SCOP: T4 endonuclease V
Endonuclease V in PDB entry 1vas, assembly 1, front view.
Endonuclease V in PDB entry 1vas, assembly 1, side view.
Endonuclease V in PDB entry 1vas, assembly 1, top view.
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DNA chain B
Name: DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')
Representative chains: B
Source organism: Tequatrovirus T4 [10665]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.96 KDa
DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3') in PDB entry 1vas, assembly 1, front view.
DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3') in PDB entry 1vas, assembly 1, side view.
DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3') in PDB entry 1vas, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')
Representative chains: C
Source organism: Tequatrovirus T4 [10665]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.99 KDa
DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3') in PDB entry 1vas, assembly 1, front view.
DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3') in PDB entry 1vas, assembly 1, side view.
DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3') in PDB entry 1vas, assembly 1, top view.
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