Structure of PDB 5jip Chain A Binding Site BS01

Receptor Information

>5jip Chain A (length=317) Species: 1502 (Clostridium perfringens)

GFAQDKNPLSTFGPDLNEFSRDVNFLTLAKNSDFIYLRASGSGTGKLRID
NKFLEFAKECRRLGIPCGAYHFAKPSKDLDSAVIQADQFIDVLQQGFGDG
DYGDLFPVLDVETPTDKSLTTTELVNWIDRFRDRFEEKTRRRLMLYTGLF
FIGLYDDFKVPGKGYPLSDMPLWIAMYTRIPSNPRIPPNVGGWKRWTMWQ
FTDEGKLDGVGSPVDLNWGPNSIDSLMPPSAVTGLNAYISGNKIFVNWTA
NKEDDLNGYNVFVNDNYAGTLPRKATKIVIDKSRFYLPKGKPIKISIEAF
DITGDFSKERTEYILDN

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: 5jip Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jip The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germination.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): D227 M230 D258 D304
• Binding residue (residue number reindexed from 1): D224 M227 D255 D301
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.2.1.17: lysozyme.

Gene Ontology

Molecular Function

• GO:0003796 lysozyme activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0046872 metal ion binding

Biological Process

• GO:0009253 peptidoglycan catabolic process
• GO:0016998 cell wall macromolecule catabolic process

External links

• PDB: RCSB:5jip, PDBe:5jip, PDBj:5jip
• PDBsum: 5jip
• PubMed: 27488615
• UniProt: O06496