Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.09 kDa 
• Atom Count: 2137 
• Modelled Residue Count: 267 
• Deposited Residue Count: 267 
• Unique protein chains: 1

1IL4

STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 9-DEAZAGUANINE

• DOI: 10.2210/pdb1IL4/pdb

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


• Deposited: 2001-05-07 Released: 2002-01-16 
• Deposition Author(s): Miller, D.J., Ravikumar, K., Shen, H., Suh, J.-K., Kerwin, S.M., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.293 
• R-Value Work: 0.222 

Literature

Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition.

Miller, D.J., Ravikumar, K., Shen, H., Suh, J.K., Kerwin, S.M., Robertus, J.D.

(2002) J Med Chem 45: 90-98

• PubMed: 11754581 
• DOI: 10.1021/jm010186s
• Primary Citation of Related Structures:  
  1IL3, 1IL9, 1IL5, 1IL4


• PubMed Abstract: 
  

Ribosome inhibiting proteins, RIPs, are a widespread family of toxic enzymes. Ricin is a plant toxin used as a poison and biological warfare agent; shiga toxin is a homologue expressed by pathogenic strains of E. coli. There is interest in creating effective antidote inhibitors to this class of enzymes. RIPs act by binding and hydrolyzing a specific adenine base from rRNA. Previous virtual screens revealed that pterins could bind in the specificity pocket of ricin and inhibit the enzyme. In this paper we explore a range of compounds that could serve as better platforms for inhibitor design. This establishes the importance of key hydrogen bond donors and acceptors for active-site complementarity. 8-Methyl-9-oxoguanine is a soluble compound that has the best inhibitory properties of any platform tested. The X-ray structure of this complex revealed that the inhibitor binds in an unexpected way that provides insight for future design. Several inhibitors of ricin were also shown to be inhibitors of shiga toxin, suggesting this program has the potential to develop effective antidotes to an important form of food poisoning.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry and Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 778712, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RICIN A CHAIN	A	267	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
9DG	A	9-DEAZAGUANINE C6 H6 N4 O FFYPRJYSJODFFD-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
9DG	IC50:  1400000   nM  BindingDB
9DG	IC50 :  1400000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.293 
• R-Value Work: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.7	α = 90
b = 68.41	β = 112.8
c = 50.16	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-07 
• Released Date: 2002-01-16 
Deposition Author(s): Miller, D.J., Ravikumar, K., Shen, H., Suh, J.-K., Kerwin, S.M., Robertus, J.D.

Revision History  

• Version 1.0: 2002-01-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance