Structure of PDB 1r4f Chain B Binding Site BS01

Receptor Information

>1r4f Chain B (length=314) Species: 5699 (Trypanosoma vivax)

SAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVT
GKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPE
NVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKY
GEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGC
PGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMYAADAL
TAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARNPEA
EFFLDMLLRSARAC

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: 1r4f Chain B Residue 329

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1r4f Leaving group activation by aromatic stacking: an alternative to general Acid catalysis.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): D10 D15 T137 D261
• Binding residue (residue number reindexed from 1): D10 D15 T137 D248
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D10 D15 D40 W83 T137 W185 N186 A260 D261
• Catalytic site (residue number reindexed from 1): D10 D15 D40 W83 T137 W185 N186 A247 D248
• Enzyme Commision number: 3.2.2.1: purine nucleosidase.

Gene Ontology

Molecular Function

• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
• GO:0046872 metal ion binding

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process

External links

• PDB: RCSB:1r4f, PDBe:1r4f, PDBj:1r4f
• PDBsum: 1r4f
• PubMed: 15050818
• UniProt: Q9GPQ4