Structure of PDB 7yrs Chain D Binding Site BS01

Receptor Information

>7yrs Chain D (length=261) Species: 47715 (Lacticaseibacillus rhamnosus)

SFSMVTRYAHSPEDIQHYDTSKLRHEFLMEKIFNPGDILLTYTYNDRMIF
GGVMPTDEPLEIKLSTELGVDFFLQRRELGIINIGGAGAITIDGRKDAMS
NQDGYYIGMGTQKVVFTSEDRDHPAKFYVVSTPAHKTYPNKKLPFATALA
KPMGDQQHLNKRTIYKYIDASQMDTCQLQMGYTVLEPGSSWNTMHARRME
TYMYFNFADPETRVFHFLGKPDETRHITLFNEQAVVNPSWSIHCGVGTTN
YAFIWAMCGEN

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 7yrs Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7yrs Lactobacillus enzymes for degradation and metabolism of glycosaminoglycan heparin
• Resolution: 2.802 Å
• Binding residue (original residue number in PDB): H200 E205 H248
• Binding residue (residue number reindexed from 1): H195 E200 H243
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 5.3.1.17: 5-dehydro-4-deoxy-D-glucuronate isomerase.

Gene Ontology

Molecular Function

• GO:0008270 zinc ion binding
• GO:0008697 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity
• GO:0016853 isomerase activity
• GO:0016861 intramolecular oxidoreductase activity, interconverting aldoses and ketoses
• GO:0046872 metal ion binding

Biological Process

• GO:0019698 D-galacturonate catabolic process
• GO:0042840 D-glucuronate catabolic process
• GO:0045490 pectin catabolic process

External links

• PDB: RCSB:7yrs, PDBe:7yrs, PDBj:7yrs
• PDBsum: 7yrs
• PubMed: 38239764
• UniProt: C2JUP1