› 4mx1

X-ray diffraction
1.59Å resolution

Structure of ricin A chain bound with 2-amino-4-oxo-N-(2-(3-phenylureido)ethyl)-3,4-dihydropteridine-7-carboxamide

Released:
DOI: 10.2210/pdb4mx1/pdb
PDB entry 4mx1 coloured by chain, front view.
PDB entry 4mx1 coloured by chain, side view.
PDB entry 4mx1 coloured by chain, top view.
Source organism: Ricinus communis
Primary publication:
Sulfur incorporation generally improves Ricin inhibition in pterin-appended glycine-phenylalanine dipeptide mimics.
Wiget PA, Manzano LA, Pruet JM, Gao G, Saito R, Monzingo AF, Jasheway KR, Robertus JD, Anslyn EV
Bioorg Med Chem Lett 23 6799-804 (2013)
PMID: 24432385

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
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand 1MX 1 x 1MX
Ligand SO4 1 x SO4
Ligand MLA 2 x MLA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P41212
Unit cell:
a: 68.102Å b: 68.102Å c: 140.532Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.227 0.261
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Endothioxopeptides: A conformational overview.
De Zotti et al. (2016)
5 other articles

1 mention without citation

Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors.
Rocha-Santos et al. (2021)