› 6mkk

X-ray diffraction
1.44Å resolution

Crystallographic solvent mapping analysis of DMSO/Mg bound to APE1

Released:
DOI: 10.2210/pdb6mkk/pdb
Model geometry
Fit model/data
PDB entry 6mkk coloured by chain, front view.
PDB entry 6mkk coloured by chain, side view.
PDB entry 6mkk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1.
Trilles R, Beglov D, Chen Q, He H, Wireman R, Reed A, Chennamadhavuni S, Panek JS, Brown LE, Vajda S, Porco JA, Kelley MR, Georgiadis MM
J Med Chem 62 1971-1988 (2019)
PMID: 30653918

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

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151054 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA repair nuclease/redox regulator APEX1, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 32.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27695 (Residues: 40-318; Coverage: 88%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand DMS 1 x DMS
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21212
Unit cell:
a: 46.697Å b: 141.487Å c: 45.334Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.183 0.212
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The multifunctional APE1 DNA repair-redox signaling protein as a drug target in human disease.
Caston et al. (2021)
2 more

1 mention without citation

Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1.
Trilles et al. (2019)