7kdu

X-ray diffraction
2.81Å 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-208797 (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 V5E4 Chain: C
Molecule details ›
Chain: C
Length: 133 amino acids
Theoretical weight: 14.26 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 45.281Å b: 76.494Å c: 101.44Å
α: 90° β: 90.92° γ: 90°
R-values:
R R work R free
0.24 0.237 0.294
Expression system: Escherichia coli