Structure of PDB 3pde Chain B Binding Site BS04

Receptor Information
>3pde Chain B (length=287) Species: 387344 (Levilactobacillus brevis ATCC 367) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLINARLIAFEDQWVPALNAPLKQAILADSQDAQLAAAMTYSVLAGGKRL
RPLLTVATMQSLGVTFVPERHWRPVMALELLHTYSLIHDDLPAMDNDALR
RGEPTNHVKFGAGMATLAGDGLLTLAFQWLTATDLPATMQAALVQALATA
AGPSGMVAGQAKDIQSEHVNLPLSQLRVLHKEKTGALLHYAVQAGLILGQ
APEAQWPAYLQFADAFGLAFQIYDDILDVVSDADEAKNTYPGKLGLIGAN
QALIDTIHSGQAALQGLPTSTQRDDLAAFFSYFDTER
Ligand information
Ligand IDDMA
InChIInChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)
InChIKeyCBIDRCWHNCKSTO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCOP(=O)(O)OP(=O)(O)O)C
ACDLabs 10.04O=P(OP(=O)(OC/C=C(/C)C)O)(O)O
OpenEye OEToolkits 1.5.0CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C
CACTVS 3.341CC(C)=CCO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CC(C)=CCO[P](O)(=O)O[P](O)(O)=O
FormulaC5 H12 O7 P2
NameDIMETHYLALLYL DIPHOSPHATE
ChEMBLCHEMBL343480
DrugBankDB01785
ZINCZINC000008215740
PDB chain3pde Chain B Residue 312 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pde Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		S85 D89 R100 K183
Binding residue
(residue number reindexed from 1)		S85 D89 R100 K183
Annotation score4
Enzymatic activity
Enzyme Commision number 2.5.1.10: (2E,6E)-farnesyl diphosphate synthase.
Gene Ontology
Molecular Function
GO:0004337 geranyltranstransferase activity
GO:0004659 prenyltransferase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0045337 farnesyl diphosphate biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3pde, PDBe:3pde, PDBj:3pde
PDBsum3pde
PubMed23493556
UniProtQ03RR4

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