Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.05 kDa 
• Atom Count: 2065 
• Residue Count: 257 
• Unique protein chains: 1

3EJ5

complex of Ricin A chain and pyrimidine-based inhibitor

• DOI: 10.2210/pdb3EJ5/pdb

• Classification: HYDROLASE
• Organism(s): Ricinus communis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-17 Released: 2009-04-07 
• Deposition Author(s): Bai, Y., Monzingo, A.F., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 

Literature

The X-ray structure of ricin A chain with a novel inhibitor

Bai, Y., Monzingo, A.F., Robertus, J.D.

(2009) Arch Biochem Biophys 483: 23-28

• PubMed: 19138659 
• DOI: 10.1016/j.abb.2008.12.013
• Primary Citation of Related Structures:  
  3EJ5


• PubMed Abstract: 
  

Ricin is a potent heterodimeric cytotoxin; the B chain binds eucaryotic cell surfaces aiding uptake and the A chain, RTA, reaches the cytoplasm where it enzymatically depurinates a key ribosomal adenine, inhibiting protein synthesis. Ricin is known to be an agent in bioterrorist repertoires and there is great interest in finding, or creating, efficacious inhibitors of the toxin as potential antidotes. We have previously identified two families of bicyclic RTA inhibitors, pterins and purines. Both classes have poor solubility which impairs inhibitor development. Here we report the use of 2-amino-4,6-dihydroxy-pyrimidines as RTA inhibitors. Unlike previously observed single ring inhibitor platforms, these displace Tyr 80 and bind deep in the RTA specificity pocket. These compounds are at least 10 times more soluble than pterin-based inhibitors and appear to be useful new class of ricin inhibitors.

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Organizational Affiliation: 

Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas, Austin, 78712, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin A chain	X	257	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EJ5	X	4-[3-(2-amino-4-hydroxy-6-oxo-1,6-dihydropyrimidin-5-yl)propyl]benzoic acid C14 H15 N3 O4 GBBVOAWLGQEGEW-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EJ5	IC50:  270000   nM  Binding MOAD
EJ5	IC50 :  270000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.642	α = 90
b = 68.006	β = 112.97
c = 49.675	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-17 
• Released Date: 2009-04-07 
Deposition Author(s): Bai, Y., Monzingo, A.F., Robertus, J.D.

Revision History 

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description