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: 29.14 kDa 
• Atom Count: 2172 
• Residue Count: 258 
• Unique protein chains: 1

3PX8

RTA in complex with 7-carboxy-pterin

• DOI: 10.2210/pdb3PX8/pdb

• Classification: hydrolase/inhibitor
• Organism(s): Ricinus communis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-09 Released: 2011-06-22 
• Deposition Author(s): Jasheway, K.R., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.233 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

7-Substituted pterins provide a new direction for ricin A chain inhibitors.

Pruet, J.M., Jasheway, K.R., Manzano, L.A., Bai, Y., Anslyn, E.V., Robertus, J.D.

(2011) Eur J Med Chem 46: 3608-3615

• PubMed: 21641093 
• DOI: 10.1016/j.ejmech.2011.05.025
• Primary Citation of Related Structures:  
  3PX8, 3PX9


• PubMed Abstract: 
  

Ricin is a potent toxin found in castor seeds. The A chain, RTA, enzymaticlly depurinates a specific adenosine in ribosomal RNA, inhibiting protein synthesis. Ricin is a known chemical weapons threat having no effective antidote. This makes the discovery of new inhibitors of great importance. We have previously used 6-substituted pterins, such as pteroic acid, as an inhibitor platform with moderate success. We now report the success of 7-carboxy pterin (7CP) as an RTA inhibitor; its binding has been monitored using both kinetic and temperature shift assays and by X-ray crystallography. We also discuss the synthesis of various derivatives of 7CP, and their binding affinity and inhibitory effects, as part of a program to make effective RTA inhibitors.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A1590, Austin, TX 78712, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Preproricin	X	258	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
JP2	X	2-amino-4-oxo-1,4-dihydropteridine-7-carboxylic acid C7 H5 N5 O3 NZLJLZVXWBEGCE-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
JP2	IC50 :  230000   nM  PDBBind
JP2	IC50:  230000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.233 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.662	α = 90
b = 67.567	β = 112.78
c = 49.41	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-09 
• Released Date: 2011-06-22 
Deposition Author(s): Jasheway, K.R., Robertus, J.D.

Revision History 

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-21
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Refinement description