Structure of PDB 3krc Chain D Binding Site BS01

Receptor Information

>3krc Chain D (length=277) Species: 34256 (Mentha x piperita)

MFDFDGYMLRKAKSVNKALEAAVQMKEPLKIHESMRYSLLAGGKRVRPML
CIAACELVGGDESTAMPAACAVEMIHTMSLMHDDLPCMDNDDLRRGKPTN
HMAFGESVAVLAGDALLSFAFEHVAAATKGAPPERIVRVLGELAVSIGSE
GLVAGQVVDVCSEGMAEVGLDHLEFIHHHKTAALLQGSVVLGAILGGGKE
EEVAKLRKFANCIGLLFQVVDDILDVTTTYPKLIGVEKSKEFADRLNREA
QEQLLHFHPHRAAPLIALANYIAYRDN

Ligand information

• Ligand ID: IPE
• InChI: InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
• InChIKey: NUHSROFQTUXZQQ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: CC(=C)CCO[P](O)(=O)O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: CC(=C)CCOP(=O)(O)OP(=O)(O)O
  ACDLabs 10.04: O=P(OP(=O)(O)O)(OCC\C(=C)C)O
  OpenEye OEToolkits 1.5.0: CC(=C)CCO[P@@](=O)(O)OP(=O)(O)O
  CACTVS 3.341: CC(=C)CCO[P@](O)(=O)O[P](O)(O)=O
• Formula: C5 H12 O7 P2
• Name: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE;
  ISOPENTENYL PYROPHOSPHATE
• ChEMBL: CHEMBL356362
• DrugBank: DB04714
• ZINC: ZINC000008215654
• PDB chain: 3krc Chain D Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3krc Structure of a heterotetrameric geranyl pyrophosphate synthase from mint (Mentha piperita) reveals intersubunit regulation
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): K44 R47 H76 R95 T181 F217
• Binding residue (residue number reindexed from 1): K44 R47 H76 R95 T181 F217
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.5.1.1: dimethylallyltranstransferase.

Gene Ontology

Molecular Function

• GO:0004659 prenyltransferase activity

Biological Process

• GO:0008299 isoprenoid biosynthetic process

External links

• PDB: RCSB:3krc, PDBe:3krc, PDBj:3krc
• PDBsum: 3krc
• PubMed: 20139160
• UniProt: Q9SBR3