Structure of PDB 7vmy Chain A Binding Site BS01

Receptor Information

>7vmy Chain A (length=294) Species: 1890733 (Limnothrix sp. CACIAM 69d)

VFKSTIAPEEKLRYIGNHKQAFDIEPLYPLALFEEFVATTGDCIIECSGK
IKQDQLYPARIDLQFSDKHHFHNIHTSIDFLKRAASRTDVNLNLDILATF
LAGNFDYSKVQNILAGIDLRQNLGESKLKLFIRIGDYPAKMAVAKHLCNI
TPESEAMLRSDTLHIGFDFYLDGRSAIELYPELKKDEFNHPFIYNQLKTI
LSPEALKPLPLCNLFGIGLSPANEANVLYYHLENIEDFLSYFPINDTARR
VHDFYLQQEGSRRMWVALSESEMKAGRINNVNLYYSKAFTSQNP

Ligand information

• Ligand ID: GST
• InChI: InChI=1S/C10H20O6P2S/c1-9(2)5-4-6-10(3)7-8-19-18(14,15)16-17(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+
• InChIKey: AKIXWSDUEPPMKM-JXMROGBWSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(=CCCC(=CCSP(=O)(O)OP(=O)(O)O)C)C
  CACTVS 3.341: CC(C)=CCCC(C)=CCS[P](O)(=O)O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: CC(=CCCC(=CCS[P@](=O)(O)OP(=O)(O)O)C)C
  CACTVS 3.341: CC(C)=CCCC(/C)=C/CS[P@@](O)(=O)O[P](O)(O)=O
  ACDLabs 10.04: O=P(O)(OP(=O)(O)O)SC/C=C(/CC/C=C(\C)C)C
• Formula: C10 H20 O6 P2 S
• Name: GERANYL S-THIOLODIPHOSPHATE;
  S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE
• DrugBank: DB04702
• PDB chain: 7vmy Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7vmy LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates
• Resolution: 1.77 Å
• Binding residue (original residue number in PDB): R68 K137 A233 V235 Y237 A275 L276 S277 N290 Y292
• Binding residue (residue number reindexed from 1): R60 K129 A225 V227 Y229 A267 L268 S269 N282 Y284
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0016740 transferase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:7vmy, PDBe:7vmy, PDBj:7vmy
• PDBsum: 7vmy
• UniProt: A0A372DCN7