Structure of PDB 3aqc Chain B Binding Site BS03

Receptor Information
>3aqc Chain B (length=321) Species: 1270 (Micrococcus luteus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYKAFLNPYIIEVEKRLYECIQSDSETINKAAHHILSSGGKRVRPMFVLL
SGFLNDTQKDDLIRTAVSLELVHMASLVHDDYIDNSDMRRGNTSVHIAFD
KDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVCFGEFDQMADRF
NYPVSFTAYLRRINRKTAILIEASCHLGALSSQLDEQSTYHIKQFGHCIG
MSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLMAAIANLKEQDDDK
LEAVVKHLTSTSDDEVYQYIVSQVKQYGIEPAELLSRKYGDKAKYHLSQL
QDSNIKDYLEEIHEKMLKRVY
Ligand information
Ligand ID2DE
InChIInChI=1S/C14H26O7P2/c1-13(2)9-8-11-14(3)10-6-4-5-7-12-20-23(18,19)21-22(15,16)17/h5,7,9-10H,4,6,8,11-12H2,1-3H3,(H,18,19)(H2,15,16,17)/b7-5+,14-10+
InChIKeyAFSHNJXUHHFZPQ-XOBXVUKQSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)=CCC/C(C)=C/CC/C=C/CO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.0CC(=CCC/C(=C/CC/C=C/CO[P@](=O)(O)OP(=O)(O)O)/C)C
CACTVS 3.370CC(C)=CCCC(C)=CCCC=CCO[P](O)(=O)O[P](O)(O)=O
ACDLabs 12.01O=P(O)(O)OP(=O)(OC/C=C/CC\C=C(/C)CC\C=C(/C)C)O
OpenEye OEToolkits 1.7.0CC(=CCCC(=CCCC=CCOP(=O)(O)OP(=O)(O)O)C)C
FormulaC14 H26 O7 P2
Name(2E,6E)-7,11-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate
ChEMBLCHEMBL1229905
DrugBank
ZINCZINC000013542325
PDB chain3aqc Chain B Residue 329 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3aqc Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation.
Resolution2.61 Å
Binding residue
(original residue number in PDB)		S80 D84 E146 K170
Binding residue
(residue number reindexed from 1)		S76 D80 E142 K166
Annotation score4
Enzymatic activity
Enzyme Commision number 2.5.1.83: hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific].
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004659 prenyltransferase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0036423 hexaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) activity
GO:0046872 metal ion binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0009234 menaquinone biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3aqc, PDBe:3aqc, PDBj:3aqc
PDBsum3aqc
PubMed21068379
UniProtO66129|HEXB_MICLU Hexaprenyl-diphosphate synthase large subunit ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=hexs-b)

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