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Ligand · VIR

VIR · Virginiamycin M1

VIR, Virginiamycin M1 (C28 H35 N3 O7, 525.6 g/mol), in the MolNFT structures on GenesisL1: bound in 4 records (4 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands found with it.

Component
VIR
Formula
C28 H35 N3 O7
Class
ligand
Structures
4
PDB entries
4

Binding sites

VIR in 4 structures; the first of them:

  • 1KHR · Crystal Structure of Vat(D) in Complex with Virginiamycin and Coenzyme A · VIR A401 · binds ASN14, VAL17, TYR37, ASP39, TYR54, ILE56, GLY79, ALA80 and 8 more
  • 1N8R · Structure of large ribosomal subunit in complex with virginiamycin M · VIR A9403 · binds G2102, A2103, C2104, A2474, A2486, C2487, A2538, U2539 and 2 more
  • 1YIT · Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of… · VIR 09000 · binds G2102, A2103, C2104, A2474, A2486, C2487, A2538, U2539 and 3 more
  • 8E3O · E. coli 50S ribosome bound to solithromycin and VM1 · VIR I3002 · binds G2061, A2062, C2063, A2439, A2451, C2452, 2MA2503, PSU2504 and 2 more

Residues it binds most

A 3, ASN 3, LEU 3, TYR 3, C 3, G 3, U 3, PRO 3, ALA 3, ASP 3 (residue and the binding sites it lines).

Found with

  • CD · Cadmium ion
  • K · Potassium ion
  • MG · Magnesium ion
  • NA · Sodium ion
  • CL · Chloride ion
  • COA · Coenzyme A
  • EM1 · (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside

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