Structure of PDB 8bm3 Chain A Binding Site BS01

Receptor Information
>8bm3 Chain A (length=239) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRSIARRTAVGAALLLVMPVAVWISGWRWQPGEQSWLLKAAFWVTETVTQ
PWGVITHLILFGWFLWCLRFRIKAAFVLFAILAAAILVGQGVKSWIKDKV
QEPRPFVIWLEKTHHIPVDEFYTLKRAERGNLVKEQLAEEKNIPQYLRSH
WQKETGFAFPSGHTMFAASWALLAVGLLWPRRRTLTIAILLVWATGVMGS
RLLLGMAWPRDLVVATLISWALVAVATWLAQRICGPLTP
Ligand information
Ligand IDFPP
InChIInChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)/b14-9+,15-11+
InChIKeyVWFJDQUYCIWHTN-YFVJMOTDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)=CCCC(C)=CCCC(C)=CCO[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OC/C=C(/CC\C=C(/C)CC\C=C(/C)C)C)(OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC(=CCC/C(=C/CC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/C)/C)C
CACTVS 3.341CC(C)=CCCC(/C)=C/CCC(/C)=C/CO[P@](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCCC(=CCOP(=O)(O)OP(=O)(O)O)C)C)C
FormulaC15 H28 O7 P2
NameFARNESYL DIPHOSPHATE
ChEMBLCHEMBL69330
DrugBankDB07780
ZINCZINC000012494625
PDB chain8bm3 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8bm3 H207A mutant of E. coli PgpB, a PAP2 type phosphatidyl glycerol phosphate and C55-PP phosphatase, in complex with farnesyl pyrophosphate
Resolution3.5 Å
Binding residue
(original residue number in PDB)		Q50 V54 H57 L87 K97 R104 E154 S161 G162 H163 R201
Binding residue
(residue number reindexed from 1)		Q50 V54 H57 L87 K97 R104 E154 S161 G162 H163 R201
Annotation score5
Enzymatic activity
Enzyme Commision number 3.1.3.27: phosphatidylglycerophosphatase.
3.1.3.4: phosphatidate phosphatase.
3.6.1.27: undecaprenyl-diphosphate phosphatase.
3.6.1.75: diacylglycerol diphosphate phosphatase.
Gene Ontology
Molecular Function
GO:0000810 diacylglycerol diphosphate phosphatase activity
GO:0008195 phosphatidate phosphatase activity
GO:0008962 phosphatidylglycerophosphatase activity
GO:0016787 hydrolase activity
GO:0050380 undecaprenyl-diphosphatase activity
Biological Process
GO:0006655 phosphatidylglycerol biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0009395 phospholipid catabolic process
GO:0046474 glycerophospholipid biosynthetic process
Cellular Component
GO:0005886 plasma membrane
GO:0009279 cell outer membrane

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Biological Process
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Cellular Component
External links
PDB RCSB:8bm3, PDBe:8bm3, PDBj:8bm3
PDBsum8bm3
PubMed
UniProtP0A924|PGPB_ECOLI Phosphatidylglycerophosphatase B (Gene Name=pgpB)

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