1BR5

RICIN A CHAIN (RECOMBINANT) COMPLEX WITH NEOPTERIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.194 

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

  • 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 effecti ...

    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: 
    • Structure of Ricin A-Chain at 2.5 Angstroms
      Katzin, B.J.,Collins, E.J.,Robertus, J.D.
      (1991) Proteins 10: 251
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RICIN)
A
267Ricinus communisEC: 3.2.2.22
Find proteins for P02879 (Ricinus communis)
Go to UniProtKB:  P02879
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NEO
Query on NEO

Download SDF File 
Download CCD File 
A
NEOPTERIN
C9 H11 N5 O4
BMQYVXCPAOLZOK-INEUFUBQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NEOKi: 2000000 nM BINDINGMOAD
NEOKi: >2000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.810α = 90.00
b = 68.790β = 112.83
c = 50.090γ = 90.00
Software Package:
Software NamePurpose
UCSD-systemdata scaling
X-PLORrefinement
UCSD-systemdata reduction
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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