Structure of PDB 2ddt Chain B Binding Site BS01

Receptor Information

>2ddt Chain B (length=287) Species: 1396 (Bacillus cereus)

DTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDN
SASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVS
KWPIAEKIQYVFAKGCLSNKGFVYTKIKKNDRFVHVIGTHLQAESPASVR
TNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTL
NASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIE
NKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 2ddt Chain B Residue 309

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ddt Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): F55 N57 E99 D100
• Binding residue (residue number reindexed from 1): F48 N50 E92 D93
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.1.4.12: sphingomyelin phosphodiesterase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004620 phospholipase activity
• GO:0004767 sphingomyelin phosphodiesterase activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0031640 killing of cells of another organism

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:2ddt, PDBe:2ddt, PDBj:2ddt
• PDBsum: 2ddt
• PubMed: 16595670
• UniProt: P11889|PHL2_BACCE Sphingomyelinase C (Gene Name=sph)