1YCJ

Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate

Naur, P.Vestergaard, B.Skov, L.K.Egebjerg, J.Gajhede, M.Kastrup, J.S.

(2005) FEBS Lett 579: 1154-1160

  • DOI: 10.1016/j.febslet.2005.01.012
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The X-ray structure of the ligand-binding core of the kainate receptor GluR5 (GluR5-S1S2) in complex with (S)-glutamate was determined to 1.95 A resolution. The overall GluR5-S1S2 structure comprises two domains and is similar to the related AMPA rec ...

    The X-ray structure of the ligand-binding core of the kainate receptor GluR5 (GluR5-S1S2) in complex with (S)-glutamate was determined to 1.95 A resolution. The overall GluR5-S1S2 structure comprises two domains and is similar to the related AMPA receptor GluR2-S1S2J. (S)-glutamate binds as in GluR2-S1S2J. Distinct features are observed for Ser741, which stabilizes a highly coordinated network of water molecules and forms an interdomain bridge. The GluR5 complex exhibits a high degree of domain closure (26 degrees) relative to apo GluR2-S1S2J. In addition, GluR5-S1S2 forms a novel dimer interface with a different arrangement of the two protomers compared to GluR2-S1S2J.


    Organizational Affiliation

    Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ionotropic glutamate receptor 5A, B257Rattus norvegicusMutation(s): 0 
Gene Names: Grik1
Find proteins for P22756 (Rattus norvegicus)
Explore P22756 
Go to UniProtKB:  P22756
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLEC50:  66000   nM  BindingDB
GGLEC50:  73000   nM  BindingDB
GGLKi:  140   nM  BindingDB
GGLKi:  330   nM  BindingDB
GGLKi:  331   nM  BindingDB
GGLKi:  332   nM  BindingDB
GGLEC50:  130000   nM  BindingDB
GGLEC50:  35200   nM  BindingDB
GGLEC50:  140000   nM  BindingDB
GGLKi:  701   nM  BindingDB
GGLEC50:  75000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.714α = 90
b = 57.901β = 102.51
c = 88.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-23
    Changes: Source and taxonomy