› 3cfp

X-ray diffraction
2.5Å resolution

Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 1

Released:
DOI: 10.2210/pdb3cfp/pdb
PDB entry 3cfp coloured by chain, front view.
PDB entry 3cfp coloured by chain, side view.
PDB entry 3cfp coloured by chain, top view.
Source organism: Escherichia phage RB69
Entry authors: Wang J, Klimenko D, Wang M, Steitz TA, Konigsberg WH

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116136 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed DNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 909 amino acids
Theoretical weight: 105.41 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
DNA (5'-D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.55 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.24 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 4 x CA
Ligand CL 1 x CL
Ligand TTP 1 x TTP
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 80.726Å b: 117.281Å c: 126.813Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.267
Expression systems:
  • Escherichia coli
  • Not provided

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