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Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit

X-ray diffraction
2.2Å resolution
PDB entry 4f5r coloured by chain, front view.
PDB entry 4f5r coloured by chain, side view.
PDB entry 4f5r 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: 21276.11 Å2
Buried surface area: 4353.0 Å2
Dissociation area: 623.87 Å2
Dissociation energy (ΔGdiss): 13.02 kcal/mol
Dissociation entropy (TΔSdiss): 8.1 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117464
Assembly 2
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Assembly Name: DNA polymerase beta and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 19887.89 Å2
Buried surface area: 4992.64 Å2
Dissociation area: 608.96 Å2
Dissociation energy (ΔGdiss): 14.4 kcal/mol
Dissociation entropy (TΔSdiss): 8.03 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117464

Macromolecules

DNA polymerase beta
Chains: A, B
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 4f5r, assembly 1, front view.
DNA polymerase beta in PDB entry 4f5r, assembly 1, side view.
DNA polymerase beta in PDB entry 4f5r, assembly 1, top view.
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DNA chains C, D
Name: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
Representative chains: C, 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 4f5r, assembly 1, front view.
DNA (5'-D(P*GP*TP*CP*GP*G)-3') in PDB entry 4f5r, assembly 1, side view.
DNA (5'-D(P*GP*TP*CP*GP*G)-3') in PDB entry 4f5r, assembly 1, top view.
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DNA chains G, P
Name: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
Representative chains: G, 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 4f5r, assembly 1, front view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') in PDB entry 4f5r, assembly 1, side view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') in PDB entry 4f5r, assembly 1, top view.
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DNA chains F, T
Name: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Representative chains: F, 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 4f5r, 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 4f5r, 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 4f5r, assembly 1, top view.
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