Structure of PDB 2pz0 Chain A Binding Site BS02

Receptor Information
>2pz0 Chain A (length=239) Species: 273068 (Caldanaerobacter subterraneus subsp. tengcongensis MB4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTLVIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDGHLVVIHD
ETVDRTTNGEGFVKDFTLEEIKKLDAGIKFGEKFAGERIPTLYEVFELIG
DKDFLVNIEIKSGIVLYPGIEEKLIKAIKEYNFEERVIISSFNHYSLRDV
KKMAPHLKIGLLYQCGLVEPWHMALRMEAYSLHPFYFNIIPELVEGCKKN
GVKLFPWTVDRKEDMERMIKAGVDGIITDDPETLINLVR
Ligand information
Ligand IDGOL
InChIInChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
InChIKeyPEDCQBHIVMGVHV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C(C(CO)O)O
ACDLabs 12.01
CACTVS 3.370		OCC(O)CO
FormulaC3 H8 O3
NameGLYCEROL;
GLYCERIN;
PROPANE-1,2,3-TRIOL
ChEMBLCHEMBL692
DrugBankDB09462
ZINCZINC000000895048
PDB chain2pz0 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2pz0 Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism.
Resolution1.91 Å
Binding residue
(original residue number in PDB)		H17 E44 F152 L172 W217
Binding residue
(residue number reindexed from 1)		H7 E34 F142 L162 W207
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H17 R18 E44 D46 H59 E119 K121 D239
Catalytic site (residue number reindexed from 1) H7 R8 E34 D36 H49 E109 K111 D229
Enzyme Commision number 3.1.4.46: glycerophosphodiester phosphodiesterase.
Gene Ontology
Molecular Function
GO:0008081 phosphoric diester hydrolase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0006629 lipid metabolic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:2pz0, PDBe:2pz0, PDBj:2pz0
PDBsum2pz0
PubMed18214974
UniProtQ8RB32|GDPD_CALS4 Glycerophosphodiester phosphodiesterase (Gene Name=UgpQ)

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