Structure of PDB 2vg3 Chain D Binding Site BS01

Receptor Information
>2vg3 Chain D (length=283) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRIP
ADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIK
WLSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSR
PRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVA
AGRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAE
YIFQDKLWPDYDRRDLWAACEEYASRTRRFGSA
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 chain2vg3 Chain D Residue 1298 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vg3 The structural basis of chain length control in Rv1086.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		D76 G77 N78 G79 R80 R89 H93 A119 R127 N139
Binding residue
(residue number reindexed from 1)		D63 G64 N65 G66 R67 R76 H80 A106 R114 N126
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D76 H93 I187
Catalytic site (residue number reindexed from 1) D63 H80 I174
Enzyme Commision number 2.5.1.86: trans,polycis-decaprenyl diphosphate synthase.
2.5.1.87: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific].
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004659 prenyltransferase activity
GO:0008834 di-trans,poly-cis-undecaprenyl-diphosphate synthase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0030145 manganese ion binding
GO:0033850 Z-farnesyl diphosphate synthase activity
GO:0045547 dehydrodolichyl diphosphate synthase activity
GO:0046872 metal ion binding
GO:0052923 all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity
Biological Process
GO:0016094 polyprenol biosynthetic process
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vg3, PDBe:2vg3, PDBj:2vg3
PDBsum2vg3
PubMed18597781
UniProtP9WFF7|DPDS_MYCTU Decaprenyl diphosphate synthase (Gene Name=uppS)

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