Crystal structure of the ATP binding domain of S. aureus gyrb complexed with a fragment

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).

Ligands and binding sites

• 54X · 5-(thiophen-2-yl)thieno[2,3-d]pyrimidin-4(1H)-one · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · chains B
• CL · Chloride ion · ion · chains A
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 226 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

• 5CTU · Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment · the same entry in another collection · chain A against A, TM-score 1.00
• P0A0K8 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0A0K8) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P0A0K8
• Elsewhere: RCSB PDB 5CTU · PDBe 5CTU · UniProt P0A0K8