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Open ternary complex of R283K DNA polymerase beta with a metal free dCTP analog

X-ray diffraction
1.8Å resolution
PDB entry 4f5n coloured by chain, front view.
PDB entry 4f5n coloured by chain, side view.
PDB entry 4f5n coloured by chain, top view.
Source organisms:
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: 21073.14 Å2
Buried surface area: 4313.35 Å2
Dissociation area: 887.93 Å2
Dissociation energy (ΔGdiss): 23.39 kcal/mol
Dissociation entropy (TΔSdiss): 9.79 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117460

Macromolecules

DNA polymerase beta
Chain: A
Length: 335 amino acids
Theoretical weight: 38.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06746 (Residues: 1-335; Coverage: 100%)
Gene name: POLB
Pfam:
InterPro:
CATH:
DNA polymerase beta in PDB entry 4f5n, assembly 1, front view.
DNA polymerase beta in PDB entry 4f5n, assembly 1, side view.
DNA polymerase beta in PDB entry 4f5n, assembly 1, top view.
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DNA chain T
Name: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Representative chains: T
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 16 nucleotides
Theoretical weight: 4.87 KDa
DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 4f5n, assembly 1, front view.
DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 4f5n, assembly 1, side view.
DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') in PDB entry 4f5n, assembly 1, top view.
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DNA chain P
Name: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
Representative chains: P
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') in PDB entry 4f5n, assembly 1, front view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') in PDB entry 4f5n, assembly 1, side view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') in PDB entry 4f5n, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
Representative chains: D
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 5 nucleotides
Theoretical weight: 1.54 KDa
DNA (5'-D(P*GP*TP*CP*GP*G)-3') in PDB entry 4f5n, assembly 1, front view.
DNA (5'-D(P*GP*TP*CP*GP*G)-3') in PDB entry 4f5n, assembly 1, side view.
DNA (5'-D(P*GP*TP*CP*GP*G)-3') in PDB entry 4f5n, assembly 1, top view.
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