Pre-catalytic ternary complex of human DNA polymerase beta with gapped DNA substrate incoming (-)ftc-tp and CA2+.

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).

Ligands and binding sites

• 1RY · [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, P, T
• NA · Sodium ion · metal · 5 copies · chains A, P, D, T
• CA · Calcium ion · metal · chains A
• ACT · Acetate ion · additive · 3 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–T · 536 Ų buried · 12 hydrogen bonds · protein-nucleic
• P–T · 470 Ų buried · 38 hydrogen bonds · nucleic-nucleic
• A–D · 379 Ų buried · 7 hydrogen bonds · protein-nucleic
• A–P · 319 Ų buried · 8 hydrogen bonds · protein-nucleic
• D–T · 230 Ų buried · 19 hydrogen bonds · nucleic-nucleic

Compared structures

• 5U2T · Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate… · the same entry in another collection · chain A against A, TM-score 1.00
• P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P06746
• Elsewhere: RCSB PDB 5U2T · PDBe 5U2T · UniProt P06746