› 7mlo

X-ray diffraction
1.65Å resolution

Crystal structure of ricin A chain in complex with 5-mesitylthiophene-2-carboxylic acid

Released:
DOI: 10.2210/pdb7mlo/pdb
PDB entry 7mlo coloured by chain, front view.
PDB entry 7mlo coloured by chain, side view.
PDB entry 7mlo 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 Chains: A, B
Molecule details ›
Chains: A, B
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

3 bound ligands:
Ligand ZJ7 2 x ZJ7
Ligand EDO 3 x EDO
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21
Unit cell:
a: 38.407Å b: 56.496Å c: 126.903Å
α: 90° β: 93.34° γ: 90°
R-values:
R R work R free
0.211 0.21 0.238
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)