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Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with dGTP

X-ray diffraction
1.9Å resolution
PDB entry 6nku coloured by chain, front view.
PDB entry 6nku coloured by chain, side view.
PDB entry 6nku coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
3 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA polymerase beta and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 19715.68 Å2
Buried surface area: 6837.22 Å2
Dissociation area: 1,576.09 Å2
Dissociation energy (ΔGdiss): 23.49 kcal/mol
Dissociation entropy (TΔSdiss): 11.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120342

Macromolecules

DNA polymerase beta
Chain: A
Length: 335 amino acids
Theoretical weight: 38.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06746 (Residues: 1-335; Coverage: 100%)
Gene name: POLB
Pfam:
InterPro:
DNA polymerase beta in PDB entry 6nku, assembly 1, front view.
DNA polymerase beta in PDB entry 6nku, assembly 1, side view.
DNA polymerase beta in PDB entry 6nku, assembly 1, top view.
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DNA chain T
Name: DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Representative chains: T
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 16 nucleotides
Theoretical weight: 4.86 KDa
DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 6nku, assembly 1, front view.
DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 6nku, assembly 1, side view.
DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 6nku, assembly 1, top view.
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DNA chain P
Name: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3')
Representative chains: P
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3') in PDB entry 6nku, assembly 1, front view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3') in PDB entry 6nku, assembly 1, side view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3') in PDB entry 6nku, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(P*TP*TP*CP*GP*G)-3')
Representative chains: D
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 5 nucleotides
Theoretical weight: 1.51 KDa
DNA (5'-D(P*TP*TP*CP*GP*G)-3') in PDB entry 6nku, assembly 1, front view.
DNA (5'-D(P*TP*TP*CP*GP*G)-3') in PDB entry 6nku, assembly 1, side view.
DNA (5'-D(P*TP*TP*CP*GP*G)-3') in PDB entry 6nku, assembly 1, top view.
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