QUINAZOLINEDIONE(PD 0305970)-DNA cleavage complex of topoisomerase IV from S. pneumoniae

Structure

x-ray diffraction · 6 distinct chains · 48% helix, 17% strand (DSSP).

Ligands and binding sites

• PDQ · 3-amino-7-{(3R)-3-[(1S)-1-aminoethyl]pyrrolidin-1-yl}-1-cyclopropyl-6-fluoro-8-methylquinazoline-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B, E, F, H, G
• MG · Magnesium ion · metal · 4 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Interfaces

14 interfaces between chains.

• A–B · 3044 Ų buried · 39 hydrogen bonds · protein-protein
• A–F · 857 Ų buried · 18 hydrogen bonds · protein-nucleic
• B–H · 841 Ų buried · 16 hydrogen bonds · protein-nucleic
• B–G · 721 Ų buried · 10 hydrogen bonds · protein-nucleic
• A–E · 714 Ų buried · 15 hydrogen bonds · protein-nucleic

Compared structures

• 4Z4Q · Quinazolinedione(PD 0305970)-DNA cleavage complex of topoisomerase IV from S. pneumoniae · the same entry in another collection · chain H against H, TM-score 1.00
• P72525 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit a (P72525) · a predicted model of the same protein · chain A against A, TM-score 0.68
• Q59961 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit B (Q59961) · a predicted model of the same protein · chain B against A, TM-score 0.32

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 Q59961
• Every structure of UniProt P72525
• Elsewhere: RCSB PDB 4Z4Q · PDBe 4Z4Q · UniProt Q59961 · UniProt P72525