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Human PARP-1 zinc finger 1 (Zn1) bound to DNA

X-ray diffraction
2.64Å resolution
PDB entry 3oda coloured by chain, front view.
PDB entry 3oda coloured by chain, side view.
PDB entry 3oda coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
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: 12578.16 Å2
Buried surface area: 2918.15 Å2
Dissociation area: 1,009.02 Å2
Dissociation energy (ΔGdiss): -7.2 kcal/mol
Dissociation entropy (TΔSdiss): 20.56 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-116642
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: 12706.56 Å2
Buried surface area: 2985.24 Å2
Dissociation area: 1,034.81 Å2
Dissociation energy (ΔGdiss): -9.19 kcal/mol
Dissociation entropy (TΔSdiss): 20.62 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-116642
Assembly 3
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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: 12844.47 Å2
Buried surface area: 2995.21 Å2
Dissociation area: 1,038.09 Å2
Dissociation energy (ΔGdiss): -7.63 kcal/mol
Dissociation entropy (TΔSdiss): 20.25 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116642
Assembly 4
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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: 12587.04 Å2
Buried surface area: 3034.59 Å2
Dissociation area: 1,061.49 Å2
Dissociation energy (ΔGdiss): -7.81 kcal/mol
Dissociation entropy (TΔSdiss): 20.61 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-116642

Macromolecules

Poly [ADP-ribose] polymerase 1, processed N-terminus
Chains: A, B, C, D, E, F, G, H
Length: 116 amino acids
Theoretical weight: 13.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09874 (Residues: 2-96; Coverage: 9%)
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 3oda, assembly 1, front view.
Poly [ADP-ribose] polymerase 1, processed N-terminus in PDB entry 3oda, assembly 1, side view.
Poly [ADP-ribose] polymerase 1, processed N-terminus in PDB entry 3oda, assembly 1, top view.
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DNA chains I, J, K, L, M, N, O, P
Name: 5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3'
Representative chains: I, J, K, L, M, N, O, P
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.05 KDa
5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3' in PDB entry 3oda, assembly 1, front view.
5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3' in PDB entry 3oda, assembly 1, side view.
5'-D(*GP*CP*CP*TP*GP*CP*AP*GP*GP*C)-3' in PDB entry 3oda, assembly 1, top view.
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