Crystal structure of catalytically inactive H270A virginiamycin B lyase from staphylococcus aureus with quinupristin

Structure

x-ray diffraction · 2 distinct chains · 1% helix, 49% strand (DSSP).

Ligands and binding sites

• DOL · 5-(2-diethylamino-ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone · ligand · 2 copies · chains A, C, B, D
• MHT · (3R)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane · ligand · 2 copies · chains A, C, B, D
• MG · Magnesium ion · metal · 4 copies · chains A, C, B, D

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

Pockets

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

Interfaces

4 interfaces between chains.

• A–C · 497 Ų buried · 6 hydrogen bonds · protein-protein
• B–D · 493 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 343 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 173 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 10 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

• 2Z2P · Crystal Structure of catalytically inactive H270A virginiamycin B lyase from… · the same entry in another collection · 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 Q53744
• Elsewhere: RCSB PDB 2Z2P · PDBe 2Z2P · UniProt Q53744