QUINOLONE(MOXIFLOXACIN)-DNA cleavage complex of topoisomerase IV from S. pneumoniae

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 16% strand (DSSP).

Ligands and binding sites

• MFX · 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid · ligand · 2 copies · chains A, B, E, F, H, G
• MG · Magnesium ion · metal · 4 copies · chains A, G, F, B, E, H

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

Pockets

17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Interfaces

13 interfaces between chains.

• A–B · 2737 Ų buried · 33 hydrogen bonds · protein-protein
• A–H · 873 Ų buried · 17 hydrogen bonds · protein-nucleic
• B–F · 831 Ų buried · 15 hydrogen bonds · protein-nucleic
• B–E · 730 Ų buried · 13 hydrogen bonds · protein-nucleic
• A–G · 698 Ų buried · 11 hydrogen bonds · protein-nucleic

Compared structures

• 4Z3O · Quinolone(Moxifloxacin)-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 B against A, TM-score 0.69
• 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 0.25

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 4Z3O · PDBe 4Z3O · UniProt Q59961 · UniProt P72525