Structure of PDB 6d9m Chain A Binding Site BS05

Receptor Information

>6d9m Chain A (length=326) Species: 10665,269799

MNIFEMLRIDQGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAI
GRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALI
NMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVI
TTFRTGTWDAYGSYIDELTGLFNYRYLDISLDREIKRADRFGSTVSMIFI
DLDFFKGVNDTHGHLVGSQVLNEMGMLLKKSVREVDIVIRYGGDEFTVML
VETGEKGAATVAERIRRSIEGHTFLAAEGFNIRLTASLGYACYPADTQSK
LELLELADKAMYQGKEQGKNCVFRAT

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: 6d9m Chain A Residue 205

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6d9m Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration.
• Resolution: 1.35 Å
• Binding residue (original residue number in PDB): D38 L39 D81
• Binding residue (residue number reindexed from 1): D201 L202 D244
• 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

Biological Process

• GO:0009253 peptidoglycan catabolic process
• GO:0016998 cell wall macromolecule catabolic process
• GO:0031640 killing of cells of another organism
• GO:0042742 defense response to bacterium
• GO:0044659 viral release from host cell by cytolysis

Cellular Component

• GO:0030430 host cell cytoplasm

External links

• PDB: RCSB:6d9m, PDBe:6d9m, PDBj:6d9m
• PDBsum: 6d9m
• PubMed: 30964001
• UniProt: P00720|ENLYS_BPT4 Endolysin (Gene Name=E);
  Q39UD1