Structure of PDB 1x09 Chain A Binding Site BS01

Receptor Information
>1x09 Chain A (length=231) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSEKLPAHGCRHVAIIMAGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAA
NNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLR
IIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQL
AEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQ
IAYAELYFTDVLWPDFDEQDFEGALNAFANR
Ligand information
Ligand IDIPE
InChIInChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
InChIKeyNUHSROFQTUXZQQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=C)CCO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0CC(=C)CCOP(=O)(O)OP(=O)(O)O
ACDLabs 10.04O=P(OP(=O)(O)O)(OCC\C(=C)C)O
OpenEye OEToolkits 1.5.0CC(=C)CCO[P@@](=O)(O)OP(=O)(O)O
CACTVS 3.341CC(=C)CCO[P@](O)(=O)O[P](O)(O)=O
FormulaC5 H12 O7 P2
Name3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE;
ISOPENTENYL PYROPHOSPHATE
ChEMBLCHEMBL356362
DrugBankDB04714
ZINCZINC000008215654
PDB chain1x09 Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1x09 Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		A26 G27 N28 G29 R30 R39 H43
Binding residue
(residue number reindexed from 1)		A18 G19 N20 G21 R22 R31 H35
Annotation score5
Binding affinityMOAD: Kd=520uM
Enzymatic activity
Catalytic site (original residue number in PDB) A26 H43 L137
Catalytic site (residue number reindexed from 1) A18 H35 L129
Enzyme Commision number 2.5.1.31: ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl- diphosphate specific].
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
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:0036094 small molecule binding
GO:0042803 protein homodimerization activity
GO:0045547 dehydrodolichyl diphosphate synthase activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0016094 polyprenol biosynthetic process
GO:0043164 Gram-negative-bacterium-type cell wall biogenesis
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1x09, PDBe:1x09, PDBj:1x09
PDBsum1x09
PubMed15788389
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

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