7kbk

X-ray diffraction
2.09Å resolution

Ricin bound to VHH antibody V6E11

Released:
Model geometry
Fit model/data

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-208792 (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 V6E11 Chain: C

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: I222
Unit cell:
a: 58.664Å b: 186.583Å c: 234.584Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.203
Expression system: Escherichia coli