Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 29.31 kDa 
• Atom Count: 2423 
• Modelled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

3LSX

Piracetam bound to the ligand binding domain of GluA3

• DOI: 10.2210/pdb3LSX/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-13 Released: 2011-03-16 
• Deposition Author(s): Ahmed, A.H., Oswald, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.222 
• R-Value Work: 0.168 
• R-Value Observed: 0.174 

Literature

Piracetam Defines a New Binding Site for Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazole-propionic Acid (AMPA) Receptors.

Ahmed, A.H., Oswald, R.E.

(2010) J Med Chem 53: 2197-2203

• PubMed: 20163115 
• DOI: 10.1021/jm901905j
• Primary Citation of Related Structures:  
  3LSW, 3LSX, 3LSL, 3LSF


• PubMed Abstract: 
  

Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system and are important potential drug targets for cognitive enhancement and the treatment of schizophrenia. Allosteric modulators of AMPA receptors promote dimerization by binding to a dimer interface and reducing desensitization and deactivation. The pyrrolidine allosteric modulators, piracetam and aniracetam, were among the first of this class of drugs to be discovered. We have determined the structure of the ligand binding domain of the AMPA receptor subtypes GluA2 and GluA3 with piracetam and a corresponding structure of GluA3 with aniracetam. Both drugs bind to GluA2 and GluA3 in a very similar manner, suggesting little subunit specificity. However, the binding sites for piracetam and aniracetam differ considerably. Aniracetam binds to a symmetrical site at the center of the dimer interface. Piracetam binds to multiple sites along the dimer interface with low occupation, one of which is a unique binding site for potential allosteric modulators. This new site may be of importance in the design of new allosteric regulators.

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Organizational Affiliation: 

Department of Molecular Medicine, Cornell University, Ithaca, New York 14853, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GluA3 S1S2 domain	A	258	Rattus norvegicus, Mus musculus This entity is chimeric	Mutation(s): 0  Gene Names: Gria3, Kiaa4184
Find proteins for P19492 (Rattus norvegicus) Explore P19492  Go to UniProtKB:  P19492
Find proteins for Q9Z2W9 (Mus musculus) Explore Q9Z2W9  Go to UniProtKB:  Q9Z2W9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU	A	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
PZI	A	2-(2-oxopyrrolidin-1-yl)acetamide C6 H10 N2 O2 GMZVRMREEHBGGF-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.222 
• R-Value Work: 0.168 
• R-Value Observed: 0.174 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.364	α = 90
b = 47.655	β = 90
c = 137.981	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-13 
• Released Date: 2011-03-16 
Deposition Author(s): Ahmed, A.H., Oswald, R.E.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-02
  Changes: Source and taxonomy