Structure of human DNA polymerase beta complexed with O6MG in the template base paired with incoming non-hydrolyzable ttp

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).

Ligands and binding sites

• 1FZ · 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine · ligand · chains A, T, P
• MG · Magnesium ion · metal · 2 copies · chains A
• NA · Sodium ion · metal · 2 copies · chains A, P, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• T–P · 483 Ų buried · 43 hydrogen bonds · nucleic-nucleic
• A–T · 443 Ų buried · 12 hydrogen bonds · protein-nucleic
• A–D · 386 Ų buried · 10 hydrogen bonds · protein-nucleic
• A–P · 313 Ų buried · 9 hydrogen bonds · protein-nucleic
• T–D · 229 Ų buried · 21 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

• 4MFF · Structure of human DNA polymerase beta complexed with O6MG in the template base paired… · 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 4MFF · PDBe 4MFF · UniProt P06746