3BKI

Crystal Structure of the GluR2 ligand binding core (S1S2J) in complex with FQX at 1.87 Angstroms

PDB DOI: https://doi.org/10.2210/pdb3BKI/pdb

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

Deposited: 2007-12-06 Released: 2008-09-16
Deposition Author(s): Cruz, L., Estebanez-Perpina, E., Pfaff, S., Borngraeber, S., Bao, N., Fletterick, R., England, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.221
R-Value Work: 0.213
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

6-Azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX) forms an irreversible bond to the active site of the GluR2 AMPA receptor.

Cruz, L.A., Estebanez-Perpina, E., Pfaff, S., Borngraeber, S., Bao, N., Blethrow, J., Fletterick, R.J., England, P.M.

(2008) J Med Chem 51: 5856-5860

PubMed: 18754610 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm701517b
Primary Citation of Related Structures:
3BKI

PubMed Abstract:
AMPA receptors mediate fast excitatory synaptic transmission and are essential for synaptic plasticity. ANQX, a photoreactive AMPA receptor antagonist, is an important biological probe used to irreversibly inactivate AMPA receptors. Here, using X-ray crystallography and mass spectroscopy, we report that ANQX forms two major products in the presence of the GluR2 AMPAR ligand-binding core (S1S2J). Upon photostimulation, ANQX reacts intramolecularly to form FQX or intermolecularly to form a covalent adduct with Glu705.

Organizational Affiliation

Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, California 94158-2517, USA.

Macromolecule Content

Total Structure Weight: 117.77 kDa
Atom Count: 8,955
Modelled Residue Count: 1,028
Deposited Residue Count: 1,052
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A [auth P], B, C, D	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19491
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FQX Query on FQX Download Ideal Coordinates CCD File SDF format, chain E [auth P] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth P] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth P] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth P], F [auth B], G [auth C], H [auth D]	[1,2,5]oxadiazolo[3,4-g]quinoxaline-6,7(5H,8H)-dione 1-oxide C₈ H₄ N₄ O₄ GBLOKWQVACPFGV-UHFFFAOYSA-N		Interactions Focus chain E [auth P] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth P] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
FQX	PDBBind: 3BKI	IC50: 7600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.221
R-Value Work: 0.213
R-Value Observed: 0.213
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.34	α = 90
b = 92.26	β = 90
c = 195.24	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

Cruz, L.

Estebanez-Perpina, E.

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-08-02
Changes: Data collection, Refinement description, Source and taxonomy
Version 1.3: 2019-09-04
Changes: Data collection
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary