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

Structure

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

Ligands and binding sites

• FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
• CAJ · ethyl 5-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]pentanoate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies
• CL · Chloride ion · ion · chains B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2714 Ų buried · 27 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 4EMW · Crystal Structure of Staphylococcus aureus bound with the covalent inhibitor EtVC-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 4EMW · PDBe 4EMW · UniProt Q2FIA5