1MS7

X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-Des-Me-AMPA at 1.97 A resolution, Crystallization in the presence of zinc acetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

GluR2 ligand-binding core complexes: importance of the isoxazolol moiety and 5-substituent for the binding mode of AMPA-type agonists

Kasper, C.Lunn, M.-L.Liljefors, T.Gouaux, E.Egebjerg, J.Kastrup, J.S.

(2002) FEBS Lett 531: 173-178

  • DOI: 10.1016/s0014-5793(02)03496-8
  • Primary Citation of Related Structures:  
    1MQD, 1MS7

  • PubMed Abstract: 
  • X-ray structures of the GluR2 ligand-binding core in complex with (S)-Des-Me-AMPA and in the presence and absence of zinc ions have been determined. (S)-Des-Me-AMPA, which is devoid of a substituent in the 5-position of the isoxazolol ring, only has limited interactions with the partly hydrophobic pocket of the ligand-binding site, and adopts an AMPA-like binding mode ...

    X-ray structures of the GluR2 ligand-binding core in complex with (S)-Des-Me-AMPA and in the presence and absence of zinc ions have been determined. (S)-Des-Me-AMPA, which is devoid of a substituent in the 5-position of the isoxazolol ring, only has limited interactions with the partly hydrophobic pocket of the ligand-binding site, and adopts an AMPA-like binding mode. The structures, in comparison with other agonist complex structures, disclose the relative importance of the isoxazolol ring and of the substituent in the 5-position for the mode of binding. A relationship appears to exist between the extent of interaction of the ligand with the hydrophobic pocket and the affinity of the ligand.


    Related Citations: 
    • Structural Basis for AMPA Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GluR2 Ligand-binding Core
      Hogner, A., Kastrup, J.S., Jin, R., Liljefors, T., Mayer, M.L., Egebjerg, J., Larsen, I., Gouaux, E.
      (2002) J Mol Biol 322: 93
    • Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core
      Armstrong, N., Gouaux, E.
      (2000) Neuron 28: 165
    • Mechanism of glutamate receptor desensitization
      Sun, Y., Olson, R., Horning, M., Armstrong, N., Mayer, M., Gouaux, E.
      (2002) Nature 417: 245
    • Probing the ligand binding domain of the GluR2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct
      Chen, G.Q., Sun, Y., Jin, R., Gouaux, E.
      (1998) Protein Sci 7: 2623

    Organizational Affiliation

    Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Universitetsparken 2, Copenhagen, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor subunit 2A, B, C263Rattus norvegicusMutation(s): 0 
Gene Names: Gria2
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
SHI PDBBind:  1MS7 IC50: 170 (nM) from 1 assay(s)
Binding MOAD:  1MS7 IC50: 170 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.723α = 90
b = 162.863β = 90
c = 47.133γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-16
    Changes: Refinement description, Source and taxonomy