1MQD

X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-Des-Me-AMPA at 1.46 A resolution. Crystallization in the presence of lithium sulfate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.180 

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

  • Primary Citation of Related Structures:  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 ...

    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: 
    • Mechanism of glutamate receptor desensitization.
      Sun, Y.,Olson, R.,Horning, M.,Armstrong, N.,Mayer, M.,Gouaux, E.
      (2002) Nature 417: 245
    • 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
    • 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.,Jin, R.,Liljefors, T.,Mayer, M.,Egebjerg, J.,Larsen, I.,Gouaux, E.
      (2002) J.Mol.Biol. 322: 93
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor subunit 2
A, B, C, D
261Rattus norvegicusGene Names: Gria2 (Glur2)
Find proteins for P19491 (Rattus norvegicus)
Go to UniProtKB:  P19491
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SHI
Query on SHI

Download SDF File 
Download CCD File 
A, B, C, D
(S)-2-AMINO-3-(3-HYDROXY-ISOXAZOL-4-YL)PROPIONIC ACID
(S)-DES-ME-AMPA
C6 H8 N2 O4
ZKLGQYGPVBFAQQ-BYPYZUCNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SHIIC50: 170 nM BINDINGMOAD
SHIIC50: 170 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.180 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.445α = 90.00
b = 47.505β = 113.70
c = 123.920γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-08-23
    Type: Refinement description, Source and taxonomy