1NNK | pdb_00001nnk

X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-ATPA at 1.85 A resolution. Crystallization with zinc ions.

• PDB DOI: https://doi.org/10.2210/pdb1NNK/pdb

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


• Deposited: 2003-01-14 Released: 2003-03-04 
• 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: 1.85 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 

Starting Model: other

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 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 29.62 kDa 
• Atom Count: 2,256 
• Modeled Residue Count: 258 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CE2	E [auth A]	3-(5-TERT-BUTYL-3-OXIDOISOXAZOL-4-YL)-L-ALANINATE C10 H15 N2 O4 PIXJURSCCVBKRF-LURJTMIESA-M
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.258	α = 90
b = 111.229	β = 90
c = 46.643	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: 2003-03-04 
Deposition Author(s): Lunn, M.-L., Hogner, A., Stensbol, T.B., Gouaux, E., Egebjerg, J., Kastrup, J.S.

Revision History  

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-08-16
  Changes: Data collection, Refinement description, Source and taxonomy
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2024-10-16
  Changes: Structure summary