› 4av1

X-ray diffraction
3.1Å resolution

Crystal structure of the human PARP-1 DNA binding domain in complex with DNA

Released:
DOI: 10.2210/pdb4av1/pdb
PDB entry 4av1 coloured by chain, front view.
PDB entry 4av1 coloured by chain, side view.
PDB entry 4av1 coloured by chain, top view.
Source organisms:
Primary publication:
The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks.
Ali AAE, Timinszky G, Arribas-Bosacoma R, Kozlowski M, Hassa PO, Hassler M, Ladurner AG, Pearl LH, Oliver AW
Nat Struct Mol Biol 19 685-692 (2012)
PMID: 22683995

Function and Biology Details

Reaction catalysed: 
NAD(+) + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117224 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Poly [ADP-ribose] polymerase 1, processed N-terminus Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 223 amino acids
Theoretical weight: 25.09 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P09874 (Residues: 5-202; Coverage: 20%)
Gene names: ADPRT, PARP1, PPOL
Sequence domains: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
Structure domains: Zinc finger, PARP-type
5'-D(*AP*AP*GP*TP*GP*TP*TP*GP*CP*AP*TP*TP)-3' Chain: X
Molecule details ›
Chain: X
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*AP*AP*TP*GP*CP*AP*AP*CP*AP*CP*TP)-3' Chain: Y
Molecule details ›
Chain: Y
Length: 12 nucleotides
Theoretical weight: 3.63 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 163.978Å b: 59.504Å c: 61.582Å
α: 90° β: 101.18° γ: 90°
R-values:
R R work R free
0.23 0.23 0.249
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

52 review citations

PARP Inhibitors: Clinical Relevance, Mechanisms of Action and Tumor Resistance.
Rose et al. (2020)
51 more

8 mentions without citation

Coordination of DNA single strand break repair.
Abbotts et al. (2017)
7 more