› 7mln

X-ray diffraction
1.52Å resolution

Crystal structure of ricin A chain in complex with 5-(o-tolyl)thiophene-2-carboxylic acid

Released:
DOI: 10.2210/pdb7mln/pdb
PDB entry 7mln coloured by chain, front view.
PDB entry 7mln coloured by chain, side view.
PDB entry 7mln coloured by chain, top view.
Source organism: Ricinus communis
Primary publication:
Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design.
Li XP, Harijan RK, Cao B, Kahn JN, Pierce M, Tsymbal AM, Roberge JY, Augeri D, Tumer NE
J Med Chem 64 15334-15348 (2021)
PMID: 34648707

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: 268 amino acids
Theoretical weight: 30.07 KDa
Source organism: Ricinus communis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02879 (Residues: 36-302; Coverage: 49%)
Sequence domains: Ribosome inactivating protein

Ligands and Environments

2 bound ligands:
Ligand ZJA 1 x ZJA
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21212
Unit cell:
a: 56.948Å b: 124.41Å c: 38.896Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.207
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Cryo-EM structure of Shiga toxin 2 in complex with the native ribosomal P-stalk reveals residues involved in the binding interaction.
Kulczyk et al. (2023)

1 mention without citation

Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design.
Li et al. (2021)