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RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite Difluorotoluene Nucleoside

X-ray diffraction
1.98Å resolution
PDB entry 3qes coloured by chain, front view.
PDB entry 3qes coloured by chain, side view.
PDB entry 3qes coloured by chain, top view.
Source organism: Escherichia phage RB69
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: DNA-directed DNA polymerase and DNA
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Multimeric state: hetero trimer
Accessible surface area: 42565.06 Å2
Buried surface area: 7370.39 Å2
Dissociation area: 2,257.04 Å2
Dissociation energy (ΔGdiss): 13.55 kcal/mol
Dissociation entropy (TΔSdiss): 12.45 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116761

Macromolecules

DNA-directed DNA polymerase
Chain: A
Length: 903 amino acids
Theoretical weight: 104.49 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Pfam:
InterPro:
CATH:
DNA-directed DNA polymerase in PDB entry 3qes, assembly 1, front view.
DNA-directed DNA polymerase in PDB entry 3qes, assembly 1, side view.
DNA-directed DNA polymerase in PDB entry 3qes, assembly 1, top view.
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DNA chain T
Name: DNA (5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
Representative chains: T
Source organism: Escherichia phage RB69 [12353]
Expression system: Not provided
Length: 18 nucleotides
Theoretical weight: 5.53 KDa
DNA (5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') in PDB entry 3qes, assembly 1, front view.
DNA (5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') in PDB entry 3qes, assembly 1, side view.
DNA (5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') in PDB entry 3qes, assembly 1, top view.
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DNA chain P
Name: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
Representative chains: P
Source organism: Escherichia phage RB69 [12353]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') in PDB entry 3qes, assembly 1, front view.
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') in PDB entry 3qes, assembly 1, side view.
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') in PDB entry 3qes, assembly 1, top view.
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