Precatalytic ternary complex of human DNA polymerase beta with gapped DNA substarte, incoming L-dctp and CA2+

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).

Ligands and binding sites

• 1S0 · 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one · ligand · chains A, T, P
• CA · Calcium ion · metal · 2 copies · chains A, P
• NA · Sodium ion · metal · 2 copies · chains A, P, D
• ACT · Acetate ion · additive · 3 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–T · 756 Ų buried · 14 hydrogen bonds · protein-nucleic
• T–P · 468 Ų buried · 40 hydrogen bonds · nucleic-nucleic
• A–D · 414 Ų buried · 9 hydrogen bonds · protein-nucleic
• A–P · 382 Ų buried · 9 hydrogen bonds · protein-nucleic
• T–D · 232 Ų buried · 19 hydrogen bonds · nucleic-nucleic

Compared structures

• 5U2R · Precatalytic ternary complex of human DNA polymerase beta with gapped DNA substarte… · 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 0.93

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 5U2R · PDBe 5U2R · UniProt P06746