DNA polymerase kappa extending beyond a bulky major BENZO[A]PYRENE adduct

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 19% strand (DSSP).

Ligands and binding sites

• VKJ · 2'-deoxy-N-[(7R,8S,9R,10S)-7,8,9-trihydroxy-7,8,9,10-tetrahydrobenzo[pqr]tetraphen-10-yl]guanosine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, C, D, B, P, T
• DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 2 copies · chains A, C, D, B, P, T
• MG · Magnesium ion · metal · 4 copies · chains A, C, B, P
• PGE · Triethylene glycol · additive · chains B

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

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

9 interfaces between chains.

• A–B · 1558 Ų buried · 36 hydrogen bonds · protein-protein
• B–T · 956 Ų buried · 16 hydrogen bonds · protein-nucleic
• A–D · 953 Ų buried · 19 hydrogen bonds · protein-nucleic
• B–P · 675 Ų buried · 21 hydrogen bonds · protein-nucleic
• A–C · 658 Ų buried · 23 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 5T14 · DNA polymerase kappa extending beyond a bulky major benzo[a]pyrene adduct · the same entry in another collection · chain C against C, TM-score 1.00
• Q9UBT6 · AlphaFold monomer V2.0 prediction for DNA polymerase kappa (Q9UBT6) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9UBT6
• Elsewhere: RCSB PDB 5T14 · PDBe 5T14 · UniProt Q9UBT6