› 3n3x

X-ray diffraction
1.7Å resolution

Crystal Structure of the complex formed between type I ribosome inactivating protein and hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 1.7 A resolution

Released:
DOI: 10.2210/pdb3n3x/pdb
PDB entry 3n3x coloured by chain, front view.
PDB entry 3n3x coloured by chain, side view.
PDB entry 3n3x coloured by chain, top view.
Source organisms:
Entry authors: Kushwaha GS, Vikram G, 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:
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 S288C
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
1 bound ligand:
Ligand GUN 1 x GUN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: R3
Unit cell:
a: 130.241Å b: 130.241Å c: 39.974Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.198 0.222
Expression system: Not provided

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