Structure of PDB 3pde Chain D Binding Site BS01

Receptor Information
>3pde Chain D (length=291) 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
APEAQWPAYLQFADAFGLAFQIYDDILDVVSSPAADEAKNTYPGKLGLIG
ANQALIDTIHSGQAALQGLPTSTQRDDLAAFFSYFDTERVN
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 D Residue 309 [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)		G47 K48 R51 H82 R101 T184 F220
Binding residue
(residue number reindexed from 1)		G47 K48 R51 H82 R101 T184 F220
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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