Precatalytic ternary complex of human DNA polymerase beta with gapped DNA substrate, incorporated (-)3TC-mp and an another incoming (-)3TC- tp nucleotide.

Structure

x-ray diffraction · 4 distinct chains · 54% helix, 12% strand (DSSP).

Ligands and binding sites

• 1RZ · Lamivudine Triphosphate · ligand · chains A
• 42E · [(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate · ligand · chains A, P, T
• NA · Sodium ion · metal · 6 copies · chains A, P, D, T
• CL · Chloride ion · ion · 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, 3 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• P–T · 475 Ų buried · 43 hydrogen bonds · nucleic-nucleic
• A–D · 389 Ų buried · 8 hydrogen bonds · protein-nucleic
• A–T · 387 Ų buried · 7 hydrogen bonds · protein-nucleic
• A–P · 309 Ų buried · 9 hydrogen bonds · protein-nucleic
• D–T · 233 Ų buried · 19 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 5TBC · Precatalytic 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 0.92

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 5TBC · PDBe 5TBC · UniProt P06746