1NNP

X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-ATPA at 1.9 A resolution. Crystallization without zinc ions.

• PDB DOI: https://doi.org/10.2210/pdb1NNP/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-01-14 Released: 2003-03-11 
• Deposition Author(s): Lunn, M.L., Hogner, A., Stensbol, T.B., Gouaux, E., Egebjerg, J., Kastrup, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.190 

Literature

Three-Dimensional Structure of the Ligand-Binding Core of GluR2 in Complex with the Agonist (S)-ATPA: Implications for Receptor Subunit Selectivity.

Lunn, M.L., Hogner, A., Stensbol, T.B., Gouaux, E., Egebjerg, J., Kastrup, J.S.

(2003) J Med Chem 46: 872-875

• PubMed: 12593667 
• DOI: https://doi.org/10.1021/jm021020+
• Primary Citation of Related Structures:  
  1NNK, 1NNP


• PubMed Abstract: 
  

  Two X-ray structures of the GluR2 ligand-binding core in complex with (S)-2-amino-3-(5-tert-butyl-3-hydroxy-4-isoxazolyl)propionic acid ((S)-ATPA) have been determined with and without Zn(2+) ions. (S)-ATPA induces a domain closure of ca. 21 degrees compared to the apo form. The tert-butyl moiety of (S)-ATPA is buried in a partially hydrophobic pocket and forces the ligand into the glutamate-like binding mode. The structures provide new insight into the molecular basis of agonist selectivity between AMPA and kainate receptors.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Pharmaceutical University of Denmark, Universitetsparken 2, DK-2100 Copenhagen, Denmark.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.09 kDa 
• Atom Count: 4,855 
• Modelled Residue Count: 516 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A, B	263	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491  Go to UniProtKB:  P19491

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CE2	D [auth A], F [auth B]	3-(5-TERT-BUTYL-3-OXIDOISOXAZOL-4-YL)-L-ALANINATE C10 H15 N2 O4 PIXJURSCCVBKRF-LURJTMIESA-M
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.190 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.728	α = 90
b = 121.469	β = 90
c = 47.105	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-11 
Deposition Author(s): Lunn, M.L., Hogner, A., Stensbol, T.B., Gouaux, E., Egebjerg, J., Kastrup, J.S.

Revision History  

• Version 1.0: 2003-03-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary