Klentaq DNA polymerase in a ternary complex with PRIMER/TEMPLATE and the fluorescent nucleotide analog bfdutp

Structure

x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).

Ligands and binding sites

• 2IU · [[(2R,3S,5R)-5-[5-(1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, B, C
• MG · Magnesium ion · metal · 3 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 1398 Ų buried · 20 hydrogen bonds · protein-nucleic
• A–B · 748 Ų buried · 20 hydrogen bonds · protein-nucleic
• B–C · 570 Ų buried · 47 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

• 7OWF · KlenTaq DNA polymerase in a ternary complex with primer/template and the fluorescent… · the same entry in another collection · chain A against A, TM-score 1.00
• P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P19821
• Elsewhere: RCSB PDB 7OWF · PDBe 7OWF · UniProt P19821