Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with ch-CH3, beta, gamma datp analogue

Structure

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

Ligands and binding sites

• HGV · 2'-deoxy-5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]adenosine · ligand · chains T, P, A
• NA · Sodium ion · metal · 3 copies · chains P, A, D
• MG · Magnesium ion · metal · chains A

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

Pockets

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

Interfaces

5 interfaces between chains.

• T–A · 709 Ų buried · 13 hydrogen bonds · protein-nucleic
• T–P · 466 Ų buried · 46 hydrogen bonds · nucleic-nucleic
• P–A · 374 Ų buried · 8 hydrogen bonds · protein-nucleic
• D–A · 372 Ų buried · 6 hydrogen bonds · protein-nucleic
• T–D · 249 Ų buried · 24 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

• 6CR6 · Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer… · the same entry in another collection · chain T against T, 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 6CR6 · PDBe 6CR6 · UniProt P06746