Structure of PDB 3d03 Chain A Binding Site BS01

Receptor Information

>3d03 Chain A (length=274) Species: 548 (Klebsiella aerogenes)

MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGD
IVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGS
DANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKP
ATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLT
MTQYRQALISTLPGTVHQVPYCHADTDPYYDLSPASCLMHRQVGEQWVSY
QHSLAHYAGPWLYDENISCPTEER

Ligand information

• Ligand ID: CO
• InChI: InChI=1S/Co/q+2
• InChIKey: XLJKHNWPARRRJB-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Co+2]
  CACTVS 3.341: [Co++]
• Formula: Co
• Name: COBALT (II) ION
• DrugBank: DB14205
• PDB chain: 3d03 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d03 Substrate-promoted formation of a catalytically competent binuclear center and regulation of reactivity in a glycerophosphodiesterase from Enterobacter aerogenes.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D8 H10 D50 H197
• Binding residue (residue number reindexed from 1): D8 H10 D50 H197
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.1.4.46: glycerophosphodiester phosphodiesterase.

Gene Ontology

Molecular Function

• GO:0004112 cyclic-nucleotide phosphodiesterase activity
• GO:0004115 3',5'-cyclic-AMP phosphodiesterase activity
• GO:0008889 glycerophosphodiester phosphodiesterase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006071 glycerol metabolic process

External links

• PDB: RCSB:3d03, PDBe:3d03, PDBj:3d03
• PDBsum: 3d03
• PubMed: 18831553
• UniProt: Q6XBH1|GPDQ_KLEAE Glycerophosphodiester phosphodiesterase GpdQ (Gene Name=gpdQ)