› 4i72

X-ray diffraction
2.05Å resolution

Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with Immucillin A

Released:
DOI: 10.2210/pdb4i72/pdb
PDB entry 4i72 coloured by chain, front view.
PDB entry 4i72 coloured by chain, side view.
PDB entry 4i72 coloured by chain, top view.
Source organism: Trypanosoma brucei brucei TREU927
Primary publication:
Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor.
Giannese F, Berg M, Van der Veken P, Castagna V, Tornaghi P, Augustyns K, Degano M
Acta Crystallogr D Biol Crystallogr 69 1553-66 (2013)
PMID: 23897478

Function and Biology Details

Reaction catalysed: 
A purine nucleoside + H(2)O = D-ribose + a purine base
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176545 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Inosine/uridine-preferring nucleoside hydrolase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 330 amino acids
Theoretical weight: 36.17 KDa
Source organism: Trypanosoma brucei brucei TREU927
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57ZL6 (Residues: 1-327; Coverage: 100%)
Gene names: Tb03.27C5.420, Tb927.3.2960
Sequence domains: Inosine-uridine preferring nucleoside hydrolase
Structure domains: Ribonucleoside hydrolase-like

Ligands and Environments

4 bound ligands:
Ligand CA 2 x CA
Ligand UA2 2 x UA2
Ligand NI 7 x NI
Ligand TRS 3 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21212
Unit cell:
a: 72.75Å b: 130.98Å c: 63.69Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.177 0.234
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases.
Degano M. (2022)
1 more

4 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
3 more