› 7y03

X-ray diffraction
1.35Å resolution

Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-2-phenylacetic acid

Released:
DOI: 10.2210/pdb7y03/pdb
PDB entry 7y03 coloured by chain, front view.
PDB entry 7y03 coloured by chain, side view.
PDB entry 7y03 coloured by chain, top view.
Source organism: Ricinus communis
Primary publication:
Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket.
Goto M, Higashi S, Ohba T, Kawata R, Nagatsu K, Suzuki S, Anslyn EV, Saito R
Biochem Biophys Res Commun 627 1-4 (2022)
PMID: 35998389

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 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 Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 30.9 KDa
Source organism: Ricinus communis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P02879 (Residues: 36-302; Coverage: 49%)
Sequence domains: Ribosome inactivating protein

Ligands and Environments

2 bound ligands:
Ligand IF4 2 x IF4
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P41212
Unit cell:
a: 67.525Å b: 67.525Å c: 141.432Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.215 0.238
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor.
Goto et al. (2023)