› 3n2d

X-ray diffraction
2.22Å resolution

Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution

Released:
DOI: 10.2210/pdb3n2d/pdb
PDB entry 3n2d coloured by chain, front view.
PDB entry 3n2d coloured by chain, side view.
PDB entry 3n2d coloured by chain, top view.
Source organisms:
Entry authors: Kushwaha GS, Prem Kumar R, Sinha M, Bhushan A, 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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112980 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 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:
Large ribosomal subunit protein P2B Chain: B
Molecule details ›
Chain: B
Length: 6 amino acids
Theoretical weight: 639 Da
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
UniProt:
  • Canonical: P02400 (Residues: 100-105; Coverage: 6%)
Gene names: L12EIA, RPL45, RPLA4, RPP2B, YDR382W

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: R3
Unit cell:
a: 131.186Å b: 131.186Å c: 40.734Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.183 0.222
Expression system: Not provided

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