glutamate transporter homologue Glttk in complex with a photo cage compound

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural Aspects of Photopharmacology: Insight into the Binding of Photoswitchable and Photocaged Inhibitors to the Glutamate Transporter Homologue.

Arkhipova, V.Fu, H.Hoorens, M.W.H.Trinco, G.Lameijer, L.N.Marin, E.Feringa, B.L.Poelarends, G.J.Szymanski, W.Slotboom, D.J.Guskov, A.

(2021) J Am Chem Soc 143: 1513-1520

  • DOI: https://doi.org/10.1021/jacs.0c11336
  • Primary Citation of Related Structures:  
    6ZGB, 6ZL4, 6ZLH

  • PubMed Abstract: 

    Photopharmacology addresses the challenge of drug selectivity and side effects through creation of photoresponsive molecules activated with light with high spatiotemporal precision. This is achieved through incorporation of molecular photoswitches and photocages into the pharmacophore. However, the structural basis for the light-induced modulation of inhibitory potency in general is still missing, which poses a major design challenge for this emerging field of research. Here we solved crystal structures of the glutamate transporter homologue Glt Tk in complex with photoresponsive transport inhibitors-azobenzene derivative of TBOA (both in trans and cis configuration) and with the photocaged compound ONB-hydroxyaspartate. The essential role of glutamate transporters in the functioning of the central nervous system renders them potential therapeutic targets in the treatment of neurodegenerative diseases. The obtained structures provide a clear structural insight into the origins of photocontrol in photopharmacology and lay the foundation for application of photocontrolled ligands to study the transporter dynamics by using time-resolved X-ray crystallography.

  • Organizational Affiliation

    University Medical Center Groningen, Department of Radiology, Medical Imaging Center, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proton/glutamate symporter, SDF family
A, B, C
438Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0986
Membrane Entity: Yes 
Find proteins for Q5JID0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JID0 
Go to UniProtKB:  Q5JID0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JID0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on QJW

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
I [auth C]
(2~{S},3~{S})-2-azanyl-3-[(2-nitrophenyl)methoxy]butanedioic acid
C11 H12 N2 O7
Query on PGE

Download Ideal Coordinates CCD File 
C6 H14 O4
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth B],
K [auth C]
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.74α = 90
b = 115.74β = 90
c = 308.49γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description