› 3ode

X-ray diffraction
2.95Å resolution

Human PARP-1 zinc finger 2 (Zn2) bound to DNA

Released:
DOI: 10.2210/pdb3ode/pdb
PDB entry 3ode coloured by chain, front view.
PDB entry 3ode coloured by chain, side view.
PDB entry 3ode coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity.
Langelier MF, Planck JL, Roy S, Pascal JM
J Biol Chem 286 10690-701 (2011)
PMID: 21233213

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116644 (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
Molecule details ›
Chains: A, B
Length: 111 amino acids
Theoretical weight: 12.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09874 (Residues: 105-206; Coverage: 10%)
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(*CP*CP*CP*AP*AP*GP*CP*G)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 8 nucleotides
Theoretical weight: 2.4 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*GP*CP*TP*TP*GP*GP*G)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 8 nucleotides
Theoretical weight: 2.46 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P3121
Unit cell:
a: 62.804Å b: 62.804Å c: 196.049Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.199 0.244
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

51 review citations

New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs.
Gibson et al. (2012)
50 more

5 mentions without citation

What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses.
Brosey et al. (2017)
4 more