7kbi

X-ray diffraction
3.05Å resolution

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-208791 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Ricin A chain Chain: A
Molecule details ›
Chain: A
Length: 267 amino acids
Theoretical weight: 29.94 KDa
Source organism: Ricinus communis
UniProt:
  • Canonical: P02879 (Residues: 36-302; Coverage: 49%)
Sequence domains: Ribosome inactivating protein
Ricin B chain Chain: B
Molecule details ›
Chain: B
Length: 262 amino acids
Theoretical weight: 28.99 KDa
Source organism: Ricinus communis
UniProt:
  • Canonical: P02879 (Residues: 315-576; Coverage: 48%)
Sequence domains: Ricin-type beta-trefoil lectin domain
VHH antibody V5E1 Chain: C
Molecule details ›
Chain: C
Length: 134 amino acids
Theoretical weight: 14.48 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer : NEW Components: NAG, BMA
1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU R-AXIS
Spacegroup: P63
Unit cell:
a: 161.418Å b: 161.418Å c: 67.031Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.239 0.237 0.274
Expression system: Escherichia coli