1WVJ | pdb_00001wvj

Exploring the GluR2 ligand-binding core in complex with the bicyclic AMPA analogue (S)-4-AHCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.214 (Depositor) 
  • R-Value Work: 
    0.169 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Exploring the GluR2 ligand-binding core in complex with the bicyclical AMPA analogue (S)-4-AHCP

Nielsen, B.B.Pickering, D.S.Greenwood, J.R.Brehm, L.Gajhede, M.Schousboe, A.Kastrup, J.S.

(2005) FEBS J 272: 1639-1648

  • DOI: https://doi.org/10.1111/j.1742-4658.2005.04583.x
  • Primary Citation Related Structures: 
    1WVJ

  • PubMed Abstract: 

    The X-ray structure of the ionotropic GluR2 ligand-binding core (GluR2-S1S2J) in complex with the bicyclical AMPA analogue (S)-2-amino-3-(3-hydroxy-7,8-dihydro-6H-cyclohepta[d]-4-isoxazolyl)propionic acid [(S)-4-AHCP] has been determined, as well as the binding pharmacology of this construct and of the full-length GluR2 receptor. (S)-4-AHCP binds with a glutamate-like binding mode and the ligand adopts two different conformations. The K(i) of (S)-4-AHCP at GluR2-S1S2J was determined to be 185 +/- 29 nM and at full-length GluR2(R)o it was 175 +/- 8 nM. (S)-4-AHCP appears to elicit partial agonism at GluR2 by inducing an intermediate degree of domain closure (17 degrees). Also, functionally (S)-4-AHCP has an efficacy of 0.38 at GluR2(Q)i, relative to (S)-glutamate. The proximity of bound (S)-4-AHCP to domain D2 prevents full D1-D2 domain closure, which is limited by steric repulsion, especially between Leu704 and the ligand.


  • Organizational Affiliation
    • Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Copenhagen, Denmark.

Macromolecule Content 

  • Total Structure Weight: 29.93 kDa 
  • Atom Count: 2,429 
  • Modeled Residue Count: 262 
  • Deposited Residue Count: 263 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ionotropic glutamate receptor 2263Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P19491 (Rattus norvegicus)
Explore P19491 
Go to UniProtKB:  P19491
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19491
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.214 (Depositor) 
  • R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.412α = 90
b = 59.467β = 90
c = 47.845γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-08-23
    Changes: Source and taxonomy
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary