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

X-ray diffraction
2.8Å resolution
PDB entry 3odc coloured by chain, front view.
PDB entry 3odc coloured by chain, side view.
PDB entry 3odc coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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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 trimer
Accessible surface area: 7911.26 Å2
Buried surface area: 1852.87 Å2
Dissociation area: 551.17 Å2
Dissociation energy (ΔGdiss): -1.61 kcal/mol
Dissociation entropy (TΔSdiss): 9.52 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116643
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 trimer
Accessible surface area: 8435.86 Å2
Buried surface area: 1869.43 Å2
Dissociation area: 556 Å2
Dissociation energy (ΔGdiss): -2.4 kcal/mol
Dissociation entropy (TΔSdiss): 9.58 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116643

Macromolecules

Poly [ADP-ribose] polymerase 1, processed N-terminus
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
Pfam: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
InterPro:
CATH: Zinc finger, PARP-type
Poly [ADP-ribose] polymerase 1, processed N-terminus in PDB entry 3odc, assembly 1, front view.
Poly [ADP-ribose] polymerase 1, processed N-terminus in PDB entry 3odc, assembly 1, side view.
Poly [ADP-ribose] polymerase 1, processed N-terminus in PDB entry 3odc, assembly 1, top view.
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DNA chains C, E
Name: 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'
Representative chains: C, E
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 8 nucleotides
Theoretical weight: 2.4 KDa
5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3' in PDB entry 3odc, assembly 1, front view.
5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3' in PDB entry 3odc, assembly 1, side view.
5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3' in PDB entry 3odc, assembly 1, top view.
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DNA chains D, F
Name: 5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3'
Representative chains: D, F
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 8 nucleotides
Theoretical weight: 2.46 KDa
5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3' in PDB entry 3odc, assembly 1, front view.
5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3' in PDB entry 3odc, assembly 1, side view.
5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3' in PDB entry 3odc, assembly 1, top view.
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