› 3v2k

X-ray diffraction
2.07Å resolution

Crystal structure of ribosome inactivating protein from momordica balsamina complexed with the product of RNA substrate adenosine triphosphate at 2.0 A resolution

Released:
DOI: 10.2210/pdb3v2k/pdb
PDB entry 3v2k coloured by chain, front view.
PDB entry 3v2k coloured by chain, side view.
PDB entry 3v2k coloured by chain, top view.
Source organism: Momordica balsamina
Primary publication:
Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states.
Kushwaha GS, Pandey N, Sinha M, Singh SB, Kaur P, Sharma S, Singh TP
Biochim Biophys Acta 1824 679-91 (2012)
PMID: 22361570

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 GOL 1 x GOL
Ligand ADE 1 x ADE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: R3
Unit cell:
a: 130.138Å b: 130.138Å c: 39.464Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.17 0.218

Quick links

Citations

5 review citations

Ribosome-inactivating and related proteins.
Schrot et al. (2015)
4 more

1 mention without citation

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