Structure of PDB 1x07 Chain A Binding Site BS02

Receptor Information
>1x07 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]
SEKLPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAAN
NGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRI
IGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLA
EKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQI
AYAELYFTDVLWPDFDEQDFEGALNAFANRE
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 chain1x07 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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PDB1x07 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.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		M25 D26 G27 N28 G29 R30 R39 H43 A69 R77
Binding residue
(residue number reindexed from 1)		M16 D17 G18 N19 G20 R21 R30 H34 A60 R68
Annotation score5
Binding affinityMOAD: Kd=520uM
PDBbind-CN: -logKd/Ki=3.28,Kd=520uM
Enzymatic activity
Catalytic site (original residue number in PDB) D26 H43 L137
Catalytic site (residue number reindexed from 1) D17 H34 L128
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:1x07, PDBe:1x07, PDBj:1x07
PDBsum1x07
PubMed15788389
UniProtP60472|UPPS_ECOLI Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) (Gene Name=ispU)

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