› 5ilw

X-ray diffraction
1.98Å resolution

Crystal structure of the complex of type 1 Ribosome inactivating protein from Momordica balsamina with Uridine at 1.97 Angstrom resolution

Released:
DOI: 10.2210/pdb5ilw/pdb
PDB entry 5ilw coloured by chain, front view.
PDB entry 5ilw coloured by chain, side view.
PDB entry 5ilw coloured by chain, top view.
Source organism: Momordica balsamina
Primary publication:
Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with uracil and uridine.
Pandey SN, Iqbal N, Singh PK, Rastogi N, Kaur P, Sharma S, Singh TP
Proteins 87 99-109 (2019)
PMID: 30007053

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112979 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
rRNA N-glycosylase Chain: A
Molecule details ›
Chain: A
Length: 246 amino acids
Theoretical weight: 27.09 KDa
Source organism: Momordica balsamina
UniProt:
  • Canonical: D9J2T9 (Residues: 1-246; Coverage: 100%)
Gene name: RIP
Sequence domains: Ribosome inactivating protein
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand NAG 1 x NAG
Ligand URI 1 x URI
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: R3
Unit cell:
a: 130.115Å b: 130.115Å c: 40.632Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.161 0.158 0.214

Quick links

Citations

1 mention without citation

Detect, correct, retract: How to manage incorrect structural models.
Wlodawer et al. (2018)