1BR6

RICIN A CHAIN (RECOMBINANT) COMPLEX WITH PTEROIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based identification of a ricin inhibitor.

Yan, X.Hollis, T.Svinth, M.Day, P.Monzingo, A.F.Milne, G.W.Robertus, J.D.

(1997) J Mol Biol 266: 1043-1049

  • DOI: 10.1006/jmbi.1996.0865
  • Primary Citation of Related Structures:  
    1BR6, 1BR5

  • PubMed Abstract: 
  • Ricin is a potent cytotoxin which has been used widely in the construction of therapeutic agents such as immunotoxins. Recently it has been used by governments and underground groups as a poison. There is interest in identifying and designing effective inhibitors of the ricin A chain (RTA) ...

    Ricin is a potent cytotoxin which has been used widely in the construction of therapeutic agents such as immunotoxins. Recently it has been used by governments and underground groups as a poison. There is interest in identifying and designing effective inhibitors of the ricin A chain (RTA). In this study computer-assisted searches indicated that pterins might bind in the RTA active site which normally recognizes a specific adenine base on rRNA. Kinetic assays showed that pteroic acid could inhibit RTA activity with an apparent Ki of 0.6 mM. A 2.3 A crystal structure of the complex revealed the mode of binding. The pterin ring displaces Tyr80 and binds in the adenine pocket making specific hydrogen bonds to active site residues. The benzoate moiety of pteroic acid binds on the opposite side of Tyr80 making van der Waals contact with the Tyr ring and forming a hydrogen bond with Asn78. Neopterin, a propane triol derivative of pterin, also binds to RTA as revealed by the X-ray structure of its complex with RTA. Neither pterin-6-carboxylic acid nor folic acid bind to the crystal or act as inhibitors. The models observed suggest alterations to the pterin moiety which may produce more potent and specific RTA inhibitors.


    Related Citations: 
    • The Structure of Recombinant Ricin a Chain at 2.3 Angstroms
      Mlsna, D., Monzingo, A.F., Katzin, B.J., Ernst, S., Robertus, J.D.
      (1993) Protein Sci 2: 429
    • Structure of Ricin A-Chain at 2.5 Angstroms
      Katzin, B.J., Collins, E.J., Robertus, J.D.
      (1991) Proteins 10: 251

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas, Austin 78712, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RICIN)A268Ricinus communisMutation(s): 0 
EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis)
Explore P02879 
Go to UniProtKB:  P02879
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT1
Query on PT1

Download CCD File 
A
PTEROIC ACID
C14 H12 N6 O3
JOAQINSXLLMRCV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PT1Ki :  600000   nM  PDBBind
PT1Ki:  600000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.992α = 90
b = 64.366β = 107.98
c = 49.442γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description