Structure of PDB 4f86 Chain K Binding Site BS02

Receptor Information
>4f86 Chain K (length=258) Species: 324833 (Streptomyces lasalocidi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVNLRLGDVDGLYHHHYGIGAVDHAALGDPGDGGYEARLIAELHRLESAQ
AEFLLDHLGPVGPGDTLVDAGCGRGGSMVMAHQRFGCKVEGVTLSAAQAE
FGNRRARELGIDDHVRSRVCNMLDTPFEKGTVAASWNNESSMYVDLHDVF
AEHSRFLRVGGRYVTVTGCWNPRYGQPSKWVSQINAHFECNIHSRREYLR
AMADNRLVPQTVVDLTPETLPYWELRATSSLVTGIEEAFIESYRDGSFQY
VLIAADRV
Ligand information
Ligand IDGPP
InChIInChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+
InChIKeyGVVPGTZRZFNKDS-JXMROGBWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCOP(=O)(O)OP(=O)(O)O)C)C
OpenEye OEToolkits 1.5.0CC(=CCC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/C)C
CACTVS 3.341CC(C)=CCCC(/C)=C/CO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CC(C)=CCCC(C)=CCO[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OP(=O)(OC/C=C(/CC\C=C(/C)C)C)O)(O)O
FormulaC10 H20 O7 P2
NameGERANYL DIPHOSPHATE
ChEMBLCHEMBL41342
DrugBankDB02552
ZINCZINC000008215849
PDB chain4f86 Chain K Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4f86 Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation
Resolution3.0 Å
Binding residue
(original residue number in PDB)		N45 H57 H58 Y59 E181 M184 F230 R268
Binding residue
(residue number reindexed from 1)		N3 H15 H16 Y17 E139 M142 F188 R226
Annotation score5
Enzymatic activity
Enzyme Commision number 2.1.1.255: geranyl diphosphate 2-C-methyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008168 methyltransferase activity
GO:0008169 C-methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0032259 methylation
GO:0042214 terpene metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4f86, PDBe:4f86, PDBj:4f86
PDBsum4f86
PubMed23090405
UniProtD3KYU3|GPPMT_STRLS Geranyl diphosphate 2-C-methyltransferase (Gene Name=gdpmt)

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