Structure of PDB 2f9r Chain D Binding Site BS01

Receptor Information

>2f9r Chain D (length=285) Species: 58217 (Loxosceles laeta)

ADNRRPIWNLAHMVNAVAQIPDFLDLGANALEADVTFKGSVPTYTYHGTP
CDFGRDCIRWEYFNVFLKTLREYTTPGNAKYRDGFILFVLDLKTGSLSND
QVRPAGENVAKELLQNYWNNGNNGGRAYVVLSLPDIGHYEFVRGFKEVLK
KEGHEDLLEKVGYDFSGPYLPSLPTLDATHEAYKKAGVDGHIWLSDGLTN
FSPLGDMARLKEAIKSRDSANGFINKIYYWSVDKVSTTKAALDVGVDGIM
TNYPNVLIGVLKESGYNDKYRLATYDDNPWETFKN

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: 2f9r Chain D Residue 604

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2f9r Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): E32 D34 D91
• Binding residue (residue number reindexed from 1): E32 D34 D91
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H12 E32 D34 H47 G48 D52 D91 K93 W230 D233 N252
• Catalytic site (residue number reindexed from 1): H12 E32 D34 H47 G48 D52 D91 K93 W230 D233 N252
• Enzyme Commision number: 4.6.1.-

Gene Ontology

Molecular Function

• GO:0008081 phosphoric diester hydrolase activity
• GO:0016829 lyase activity
• GO:0046872 metal ion binding
• GO:0090729 toxin activity

Biological Process

• GO:0006629 lipid metabolic process
• GO:0016042 lipid catabolic process
• GO:0031640 killing of cells of another organism
• GO:0035821 modulation of process of another organism

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:2f9r, PDBe:2f9r, PDBj:2f9r
• PDBsum: 2f9r
• PubMed: 15654080
• UniProt: Q8I914|A311_LOXLA Dermonecrotic toxin LlSicTox-alphaIII1i