› 4f9n

X-ray diffraction
2.65Å resolution

Crystal structure of the complex of type I Ribosome inactivating protein from Momordica balsamina with N7-methylated guanine at 2.65 A resolution

Released:
DOI: 10.2210/pdb4f9n/pdb
PDB entry 4f9n coloured by chain, front view.
PDB entry 4f9n coloured by chain, side view.
PDB entry 4f9n coloured by chain, top view.
Source organism: Momordica balsamina
Entry authors: Yamini S, Kushwaha GS, Bhushan A, Sinha M, Kaur P, Sharma S, Singh TP

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
Macromolecules (2 distinct):
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

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand MY6 1 x MY6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: R3
Unit cell:
a: 131.428Å b: 131.428Å c: 39.808Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.17 0.169 0.196

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