1NNK

X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-ATPA at 1.85 A resolution. Crystallization with zinc ions.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Three-Dimensional Structure of the Ligand-Binding Core of GluR2 in Complex with the Agonist (S)-ATPA: Implications for Receptor Subunit Selectivity.

Lunn, M.L.Hogner, A.Stensbol, T.B.Gouaux, E.Egebjerg, J.Kastrup, J.S.

(2003) J.Med.Chem. 46: 872-875

  • DOI: 10.1021/jm021020+
  • Primary Citation of Related Structures:  1NNP
  • Also Cited By: 3PD9

  • PubMed Abstract: 
  • Two X-ray structures of the GluR2 ligand-binding core in complex with (S)-2-amino-3-(5-tert-butyl-3-hydroxy-4-isoxazolyl)propionic acid ((S)-ATPA) have been determined with and without Zn(2+) ions. (S)-ATPA induces a domain closure of ca. 21 degrees ...

    Two X-ray structures of the GluR2 ligand-binding core in complex with (S)-2-amino-3-(5-tert-butyl-3-hydroxy-4-isoxazolyl)propionic acid ((S)-ATPA) have been determined with and without Zn(2+) ions. (S)-ATPA induces a domain closure of ca. 21 degrees compared to the apo form. The tert-butyl moiety of (S)-ATPA is buried in a partially hydrophobic pocket and forces the ligand into the glutamate-like binding mode. The structures provide new insight into the molecular basis of agonist selectivity between AMPA and kainate receptors.


    Related Citations: 
    • 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, R.,Jin, R.,Gouaux, E.
      (1998) Protein Sci. 7: 2623
    • Mechanism of glutamate receptor desensitization.
      Sun, Y.,Olson, R.,Horning, M.,Armstrong, N.,Mayer, M.,Gouaux, E.
      (2002) Nature 417: 245
    • 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


    Organizational Affiliation

    Department of Medicinal Chemistry, Pharmaceutical University of Denmark, Universitetsparken 2, DK-2100 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor 2
A
263Rattus 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
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CE2
Query on CE2

Download SDF File 
Download CCD File 
A
3-(5-TERT-BUTYL-3-OXIDOISOXAZOL-4-YL)-L-ALANINATE
(S)-ATPA, (S)-2-AMINO-3-(3-HYDROXY-5-TERT-BUTYL-ISOXAZOL-4-YL)PROPIONIC ACID
C10 H15 N2 O4
PIXJURSCCVBKRF-LURJTMIESA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CE2IC50: 3500 nM BINDINGMOAD
CE2IC50: 3500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.258α = 90.00
b = 111.229β = 90.00
c = 46.643γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-16
    Type: Data collection, Refinement description, Source and taxonomy