3ca0

X-ray diffraction
1.95Å resolution

Sambucus nigra agglutinin II (SNA-II), hexagonal crystal form

Released:

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152551 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (5 distinct):
Nigrin b B chain Chain: A
Molecule details ›
Chain: A
Length: 258 amino acids
Theoretical weight: 28.44 KDa
Source organism: Sambucus nigra
UniProt:
  • Canonical: P33183 (Residues: 306-563; Coverage: 48%)
Sequence domains: Ricin-type beta-trefoil lectin domain
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, XYP, MAN, FUC
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer : NEW Components: NAG, FUC
2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P6422
Unit cell:
a: 120.204Å b: 120.204Å c: 177.34Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.171 0.194