2QS4 | pdb_00002qs4

Crystal structure of the GluR5 ligand binding core dimer in complex with LY466195 at 1.58 Angstroms resolution

PDB DOI: https://doi.org/10.2210/pdb2QS4/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-07-30 Released: 2008-08-05
Deposition Author(s): Alushin, G.M., Jane, D.E., Mayer, M.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.199 (Depositor), 0.198 (DCC)
R-Value Work:
0.158 (Depositor), 0.159 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists.

Alushin, G.M., Jane, D., Mayer, M.L.

(2011) Neuropharmacology 60: 126-134

PubMed: 20558186 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.neuropharm.2010.06.002
Primary Citation Related Structures:
2QS1, 2QS2, 2QS4

PubMed Abstract:
The availability of crystal structures for the ligand binding domains of ionotropic glutamate receptors, combined with their key role in synaptic function in the normal and diseased brain, offers a unique selection of targets for pharmaceutical research compared to other drug targets for which the atomic structure of the ligand binding site is not known. Currently only a few antagonist structures have been solved, and these reveal ligand specific conformational changes that hinder rational drug design. Here we report high resolution crystal structures for three kainate receptor GluK1 antagonist complexes which reveal new and unexpected modes of binding, highlighting the continued need for experimentally determined receptor-ligand complexes.

Organizational Affiliation

Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, NICHD, NIH, DHHS, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 118.45 kDa
Atom Count: 9,924
Modeled Residue Count: 1,011
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor, ionotropic kainate 1	A, B, C, D	258	Rattus norvegicus	Mutation(s): 1 Gene Names: Grik1, Glur5
UniProt
Find proteins for P22756 (Rattus norvegicus) Explore P22756 Go to UniProtKB: P22756
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22756
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LY5 Query on LY5 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D]	F [auth A], G [auth B], I [auth C], L [auth D]	(3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid C₁₆ H₂₄ F₂ N₂ O₄ OXQXJYQSWZFDBB-WJTVCTBASA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C]	H [auth B], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain H [auth B] Focus chain J [auth C]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth D]	E [auth A], K [auth D]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth D]