4H8I

Structure of GluK2-LBD in complex with GluAzo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A photoswitchable neurotransmitter analogue bound to its receptor.

Reiter, A.Skerra, A.Trauner, D.Schiefner, A.

(2013) Biochemistry 52: 8972-8974

  • DOI: 10.1021/bi4014402

  • PubMed Abstract: 
  • Incorporation of the azobenzene derivative gluazo, a synthetic photochromic ligand, into a kainate receptor allows for the optical control of neuronal activity. The crystal structure of gluazo bound to a dimeric GluK2 ligand-binding domain reveals on ...

    Incorporation of the azobenzene derivative gluazo, a synthetic photochromic ligand, into a kainate receptor allows for the optical control of neuronal activity. The crystal structure of gluazo bound to a dimeric GluK2 ligand-binding domain reveals one monomer in a closed conformation, occupied by gluazo, and the other in an open conformation, with a bound buffer molecule. The glutamate group of gluazo interacts like the natural glutamate ligand, while its trans-azobenzene moiety protrudes into a tunnel. This elongated cavity presumably cannot accommodate a cis-azobenzene, which explains the reversible activation of the receptor upon photoisomerization.


    Organizational Affiliation

    Munich Center for Integrated Protein Science (CIPS-M).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor, ionotropic kainate 2
A, B
259Rattus norvegicusMutation(s): 0 
Gene Names: Grik2 (Glur6)
Find proteins for P42260 (Rattus norvegicus)
Go to UniProtKB:  P42260
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
11W
Query on 11W

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A
(4R)-4-[(2E)-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-en-1-yl]-L-glutamic acid
trans-GluAzo
C20 H21 N3 O4
MUSRDKYERZDIAD-MTDKYJNHSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MES
Query on MES

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B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.609α = 90.00
b = 102.609β = 90.00
c = 282.513γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-15
    Type: Refinement description