Structure of PDB 3vc1 Chain B Binding Site BS02

Receptor Information
>3vc1 Chain B (length=278) Species: 100226 (Streptomyces coelicolor A3(2)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAPATPYQEDIARYWNNEARPVNLRLGDVDGLYHHHYGIGPVDRAALGDP
EHSEYEKKVIAELHRLESAQAEFLMDHLGQAGPDDTLVDAGCGRGGSMVM
AHRRFGSRVEGVTLSAAQADFGNRRARELRIDDHVRSRVCNMLDTPFDKG
AVTASWNNESTMYVDLHDLFSEHSRFLKVGGRYVTITGCWNPRYGQPSKW
VSQINAHFECNIHSRREYLRAMADNRLVPHTIVDLTPDTLPYWELRATSS
LVTGIEKAFIESYRDGSFQYVLIAADRV
Ligand information
Ligand IDGST
InChIInChI=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+
InChIKeyAKIXWSDUEPPMKM-JXMROGBWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCSP(=O)(O)OP(=O)(O)O)C)C
CACTVS 3.341CC(C)=CCCC(C)=CCS[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCS[P@](=O)(O)OP(=O)(O)O)C)C
CACTVS 3.341CC(C)=CCCC(/C)=C/CS[P@@](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(O)(OP(=O)(O)O)SC/C=C(/CC/C=C(\C)C)C
FormulaC10 H20 O6 P2 S
NameGERANYL S-THIOLODIPHOSPHATE;
S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE
ChEMBL
DrugBankDB04702
ZINC
PDB chain3vc1 Chain B Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vc1 Structure of Geranyl Diphosphate C-Methyltransferase from Streptomyces coelicolor and Implications for the Mechanism of Isoprenoid Modification.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		W29 R34 V36 N37 H49 Y51 M176 F222 R260
Binding residue
(residue number reindexed from 1)		W15 R20 V22 N23 H35 Y37 M162 F208 R246
Annotation score2
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:3vc1, PDBe:3vc1, PDBj:3vc1
PDBsum3vc1
PubMed22455498
UniProtQ9F1Y5|GPPMT_STRCO Geranyl diphosphate 2-C-methyltransferase (Gene Name=SCO7701)

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