Structure of DNA polymerase III, beta subunit/ beta sliding clamp from klebsiella pneumoniae, expressed with an N-terminal his-SMT3 fusion tag, in complex with griselimycin

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 44% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · chains A, B
• CA · Calcium ion · metal · chains A
• CL · Chloride ion · ion · chains A
• PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains A
• ACT · Acetate ion · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 581 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 modified, 1 covalent (nonstandard, methylation, covalent ligand).

Compared structures

• 6P81 · Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella… · the same entry in another collection · chain A against A, TM-score 1.00
• Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain A against A, TM-score 0.17

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 Q12306
• Every structure of UniProt W1BGQ6
• Elsewhere: RCSB PDB 6P81 · PDBe 6P81 · UniProt Q12306 · UniProt W1BGQ6