Crystal structure of staphylococcus aureus bound with the covalent inhibitor pethyl-vs-CoA

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).

Ligands and binding sites

• FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
• CA8 · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[4-(phenylsulfonyl)butylamino]propyl]amino]butyl] hydrogen phosphate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 3 copies · chains A, B
• CL · Chloride ion · ion · 7 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 2823 Ų buried · 31 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 4EM4 · Crystal Structure of Staphylococcus aureus bound with the covalent inhibitor Pethyl-VS-CoA · the same entry in another collection · chain A against A, TM-score 1.00
• Q2FIA5 · AlphaFold monomer V2.0 prediction for coenzyme a disulfide reductase (Q2FIA5) · a predicted model of the same protein · chain B 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 Q2FIA5
• Elsewhere: RCSB PDB 4EM4 · PDBe 4EM4 · UniProt Q2FIA5