4k8z

X-ray diffraction
2.29Å resolution

KOD Polymerase in binary complex with dsDNA

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-117723 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Homing endonuclease PI-PkoII Chain: A
Molecule details ›
Chain: A
Length: 774 amino acids
Theoretical weight: 90.06 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: P77933 (Residues: 1-1671; Coverage: 46%)
Gene names: TK0001, pol
Sequence domains:
Structure domains:
DNA (5'-D(*AP*AP*AP*TP*TP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Not provided
DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(2DA))-3') Chain: P
Molecule details ›
Chain: P
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Not provided

Ligands and Environments

3 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21212
Unit cell:
a: 144.87Å b: 111.78Å c: 67.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.218
Expression systems:
  • Escherichia coli
  • Not provided