DNA polymerase IV - DNA ternary complex 5

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).

Ligands and binding sites

• TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains F, G, H, A, B, C
• MG · Magnesium ion · metal · 4 copies · chains F, H, A, C

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

9 interfaces between chains.

• A–B · 1014 Ų buried · 24 hydrogen bonds · protein-nucleic
• F–G · 966 Ų buried · 22 hydrogen bonds · protein-nucleic
• B–C · 651 Ų buried · 63 hydrogen bonds · nucleic-nucleic
• G–H · 644 Ų buried · 62 hydrogen bonds · nucleic-nucleic
• A–C · 575 Ų buried · 20 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 5YUV · DNA polymerase IV - DNA ternary complex 5 · the same entry in another collection · chain C against C, TM-score 1.00
• Q47155 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q47155) · 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 Q47155
• Elsewhere: RCSB PDB 5YUV · PDBe 5YUV · UniProt Q47155