6ZL4

the structure of glutamate transporter homologue GltTk in complex with the photo switchable compound (cis)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

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 ...

    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: 

    Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proton/glutamate symporter, SDF family
A, B, C
438Thermococcus kodakarensisMutation(s): 0 
Gene Names: TK0986
Membrane Entity: Yes 
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU
Download Ideal Coordinates CCD File 
DA [auth C],
E [auth A],
T [auth B]		DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N		 Ligand Interaction
QM5
Query on QM5
Download Ideal Coordinates CCD File 
CA [auth C],
D [auth A],
P [auth B]		(2~{S},3~{S})-2-azanyl-3-[[4-[2-(4-methoxyphenyl)hydrazinyl]phenyl]methoxy]butanedioic acid
C18 H21 N3 O6
FVCUHYYDCQQINH-HOTGVXAUSA-N		 Ligand Interaction
1PE
Query on 1PE
Download Ideal Coordinates CCD File 
FA [auth C]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth A]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
EA [auth C]
H [auth A]
J [auth A]
Q [auth B]
U [auth B]
EA [auth C],
H [auth A],
J [auth A],
Q [auth B],
U [auth B],
V [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
JA [auth C]
KA [auth C]
LA [auth C]
AA [auth B],
BA [auth B],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
PA [auth C],
R [auth B],
S [auth B],
Z [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
GA [auth C]
HA [auth C]
IA [auth C]
K [auth A]
L [auth A]
GA [auth C],
HA [auth C],
IA [auth C],
K [auth A],
L [auth A],
M [auth A],
W [auth B],
X [auth B],
Y [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.21α = 90
b = 117.21β = 90
c = 309.41γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands--

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