› 3g5i

X-ray diffraction
2.1Å resolution

Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor

Released:
DOI: 10.2210/pdb3g5i/pdb
PDB entry 3g5i coloured by chain, front view.
PDB entry 3g5i coloured by chain, side view.
PDB entry 3g5i coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor.
Garau G, Muzzolini L, Tornaghi P, Degano M
BMC Struct Biol 10 14 (2010)
PMID: 20529317

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154394 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrimidine-specific ribonucleoside hydrolase RihA Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 312 amino acids
Theoretical weight: 33.87 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P41409 (Residues: 2-311; Coverage: 100%)
Gene names: JW0646, b0651, rihA, ybeK
Sequence domains: Inosine-uridine preferring nucleoside hydrolase
Structure domains: Ribonucleoside hydrolase-like

Ligands and Environments

3 bound ligands:
Ligand BME 1 x BME
Ligand CA 4 x CA
Ligand DNB 4 x DNB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 84.35Å b: 82.91Å c: 93.87Å
α: 90° β: 112.15° γ: 90°
R-values:
R R work R free
0.205 0.203 0.241
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases.
Degano M. (2022)
2 other articles

3 mentions without citation

Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical Uses.
Shaposhnikov et al. (2023)
2 more