Structure of PDB 2ddr Chain D Binding Site BS01

Receptor Information

>2ddr Chain D (length=298) Species: 1396 (Bacillus cereus)

DTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDN
SASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVS
KWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDS
MCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNN
DSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIA
SKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 2ddr Chain D Residue 1330

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ddr Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): F55 N57 R80 E99 D100
• Binding residue (residue number reindexed from 1): F48 N50 R73 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:2ddr, PDBe:2ddr, PDBj:2ddr
• PDBsum: 2ddr
• PubMed: 16595670
• UniProt: P11889|PHL2_BACCE Sphingomyelinase C (Gene Name=sph)