Structure of the alanine racemase from staphylococcus aureus in complex with a pyridoxal 5' phosphate-derivative

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).

Ligands and binding sites

• EOW · (6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
• NA · Sodium ion · metal · 6 copies · chains A, B
• CL · Chloride ion · ion · chains B
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, B
• ACT · Acetate ion · additive · 6 copies · chains A, B
• MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
• GOL · Glycerol · additive · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 3286 Ų buried · 34 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6G58 · Structure of the alanine racemase from Staphylococcus aureus in complex with a pyridoxal… · the same entry in another collection · chain A against A, TM-score 1.00
• P63479 · AlphaFold monomer V2.0 prediction for alanine racemase 1 (P63479) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P63479
• Elsewhere: RCSB PDB 6G58 · PDBe 6G58 · UniProt P63479