3BFT | pdb_00003bft

Structure of the ligand-binding core of GluR2 in complex with the agonist (S)-TDPA at 2.25 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BFT/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-23 Released: 2008-10-28
Deposition Author(s): Beich-Frandsen, M., Mirza, O., Vestergaard, B., Gajhede, M., Kastrup, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.250 (Depositor), 0.198 (DCC)
R-Value Work:
0.200 (Depositor), 0.196 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structures of the ligand-binding core of iGluR2 in complex with the agonists (R)- and (S)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propionic acid explain their unusual equipotency.

Beich-Frandsen, M., Pickering, D.S., Mirza, O., Johansen, T.N., Greenwood, J., Vestergaard, B., Schousboe, A., Gajhede, M., Liljefors, T., Kastrup, J.S.

(2008) J Med Chem 51: 1459-1463

PubMed: 18269227 Search on PubMed
DOI: https://doi.org/10.1021/jm701126w
Primary Citation Related Structures:
3BFT, 3BFU

PubMed Abstract:
AMPA-type ionotropic glutamate receptors generally display high stereoselectivity in agonist binding. However, the stereoisomers of 2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propionic acid (TDPA) have similar enantiopharmacology. To understand this observation, we have determined the X-ray structures of ( R)-TDPA and ( S)-TDPA in complex with the ligand-binding core of iGluR2 and investigated the binding pharmacology at AMPA and kainate receptors. Both enantiomers induce full domain closure in iGluR2 but adopt different conformations when binding to the receptor, which may explain the similar enantiopharmacology.

Organizational Affiliation

Department of Medicinal Chemistry, University of Copenhagen, Copenhagen, Denmark.

Macromolecule Content

Total Structure Weight: 88.78 kDa
Atom Count: 6,695
Modeled Residue Count: 777
Deposited Residue Count: 789
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A, B, C	263	Rattus norvegicus	Mutation(s): 0 Gene Names: Gria2, Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491 Go to UniProtKB: P19491
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19491
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S2P Query on S2P Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain O [auth C] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain O [auth C] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], O [auth C]	(2S)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propanoic acid C₅ H₇ N₃ O₃ S SEVVPWOEIHLQGH-REOHCLBHSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain O [auth C]
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], K [auth B], L [auth B], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.250 (Depositor), 0.198 (DCC)
R-Value Work: 0.200 (Depositor), 0.196 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.82	α = 90
b = 163.333	β = 90
c = 47.27	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-10-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-10-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-08-23
Changes: Refinement description, Source and taxonomy
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary