› 1il5

X-ray diffraction
2.8Å resolution

STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE (DDP)

Released:
DOI: 10.2210/pdb1il5/pdb
PDB entry 1il5 coloured by chain, front view.
PDB entry 1il5 coloured by chain, side view.
PDB entry 1il5 coloured by chain, top view.
Source organism: Ricinus communis
Primary publication:
Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition.
Miller DJ, Ravikumar K, Shen H, Suh JK, Kerwin SM, Robertus JD
J Med Chem 45 90-8 (2002)
PMID: 11754581

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 domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136287 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ricin A chain Chains: A, B
Molecule details ›
Chains: A, B
Length: 267 amino acids
Theoretical weight: 29.94 KDa
Source organism: Ricinus communis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02879 (Residues: 36-302; Coverage: 49%)
Sequence domains: Ribosome inactivating protein
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand DDP 1 x DDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P1
Unit cell:
a: 42.07Å b: 65.95Å c: 50.81Å
α: 93.9° β: 112.4° γ: 84.43°
R-values:
R R work R free
0.225 0.225 0.283
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Shiga toxins--from cell biology to biomedical applications.
Johannes et al. (2010)
8 more

3 mentions without citation

Identification of new classes of ricin toxin inhibitors by virtual screening.
Bai et al. (2010)
2 more