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Structure of Human PARP-1 bound to a DNA double strand break in complex with (2Z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide

X-ray diffraction
3.65Å resolution
PDB entry 4oqa coloured by chain, front view.
PDB entry 4oqa coloured by chain, side view.
PDB entry 4oqa coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules
1 distinct DNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Poly [ADP-ribose] polymerase 1, processed C-terminus and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 43230.91 Å2
Buried surface area: 5419.74 Å2
Dissociation area: 857.34 Å2
Dissociation energy (ΔGdiss): -2.38 kcal/mol
Dissociation entropy (TΔSdiss): 12.68 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117932
Assembly 2
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Assembly Name: Poly [ADP-ribose] polymerase 1, processed C-terminus and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 43466.84 Å2
Buried surface area: 5334.57 Å2
Dissociation area: 824.46 Å2
Dissociation energy (ΔGdiss): -2.77 kcal/mol
Dissociation entropy (TΔSdiss): 12.68 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117932

Macromolecules

Poly [ADP-ribose] polymerase 1, processed C-terminus
Chains: A, D
Length: 267 amino acids
Theoretical weight: 30.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09874 (Residues: 1-97, 207-366; Coverage: 25%)
Gene names: ADPRT, PARP1, PPOL
Pfam:
InterPro:
CATH: Zinc finger, PARP-type
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4oqa, assembly 1, front view.
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4oqa, assembly 1, side view.
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4oqa, assembly 1, top view.
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Poly [ADP-ribose] polymerase 1, processed C-terminus
Chains: C, F
Length: 505 amino acids
Theoretical weight: 57.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09874 (Residues: 518-1014; Coverage: 49%)
Gene names: ADPRT, PARP1, PPOL
Pfam:
InterPro:
CATH:
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4oqa, assembly 1, front view.
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4oqa, assembly 1, side view.
Poly [ADP-ribose] polymerase 1, processed C-terminus in PDB entry 4oqa, assembly 1, top view.
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DNA chains M, N
Name: DNA (26-MER)
Representative chains: M, N
Length: 26 nucleotides
Theoretical weight: 7.99 KDa
DNA (26-MER) in PDB entry 4oqa, assembly 1, front view.
DNA (26-MER) in PDB entry 4oqa, assembly 1, side view.
DNA (26-MER) in PDB entry 4oqa, assembly 1, top view.
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