› 5dfi

X-ray diffraction
1.63Å resolution

Human APE1 phosphorothioate substrate complex

Released:
DOI: 10.2210/pdb5dfi/pdb
PDB entry 5dfi coloured by chain, front view.
PDB entry 5dfi coloured by chain, side view.
PDB entry 5dfi coloured by chain, top view.
Source organisms:
Primary publication:
Capturing snapshots of APE1 processing DNA damage.
Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH
Nat Struct Mol Biol 22 924-31 (2015)
PMID: 26458045

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-118564 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA repair nuclease/redox regulator APEX1, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 276 amino acids
Theoretical weight: 31.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P27695 (Residues: 43-318; Coverage: 87%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(OMC)P*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 21 nucleotides
Theoretical weight: 6.4 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: V
Molecule details ›
Chain: V
Length: 21 nucleotides
Theoretical weight: 6.47 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand EDO 6 x EDO
Ligand CL 2 x CL
1 modified residue:
Ligand OMC 1 x OMC

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P1
Unit cell:
a: 44.418Å b: 60.828Å c: 73.212Å
α: 83° β: 80.53° γ: 89.12°
R-values:
R R work R free
0.168 0.167 0.195
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Base excision repair of oxidative DNA damage: from mechanism to disease.
Whitaker et al. (2017)
8 more

16 mentions without citation

Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism.
Beard et al. (2019)
15 more