› 6fbc

X-ray diffraction
1.54Å resolution

KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer.

Released:
DOI: 10.2210/pdb6fbc/pdb
PDB entry 6fbc coloured by chain, front view.
PDB entry 6fbc coloured by chain, side view.
PDB entry 6fbc coloured by chain, top view.
Source organisms:
Primary publication:
Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Kropp HM, Dürr SL, Peter C, Diederichs K, Marx A
OpenAccess logo Proc Natl Acad Sci U S A 115 9992-9997 (2018)
PMID: 30224478

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-119891 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I, thermostable Chain: A
Molecule details ›
Chain: A
Length: 541 amino acids
Theoretical weight: 61.07 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 293-832; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*(OH3))-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*CP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.94 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand XG4 1 x XG4
Ligand EDO 2 x EDO
Ligand MN 2 x MN
Ligand MG 2 x MG
1 modified residue:
Ligand D4B 1 x D4B

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P3121
Unit cell:
a: 109.23Å b: 109.23Å c: 90.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.186 0.208
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Modified nucleic acids: replication, evolution, and next-generation therapeutics.
Duffy et al. (2020)
2 more

1 mention without citation

Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Kropp et al. (2018)