› 6yk3

X-ray diffraction
1.2Å resolution

Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound ( S) - 1- [2'-Amino-2'-carboxyethyl]-5 ,7- dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 1.20A

Released:
DOI: 10.2210/pdb6yk3/pdb
PDB entry 6yk3 coloured by chain, front view.
PDB entry 6yk3 coloured by chain, side view.
PDB entry 6yk3 coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions.
Frydenvang K, Pickering DS, Kshirsagar GU, Chemi G, Gemma S, Sprogøe D, Kærn AM, Brogi S, Campiani G, Butini S, Kastrup JS
ACS Chem Neurosci 11 1791-1800 (2020)
PMID: 32437601

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148607 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glutamate receptor 2 Chain: A
Molecule details ›
Chain: A
Length: 264 amino acids
Theoretical weight: 29.28 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P19491 (Residues: 413-527, 653-797; Coverage: 30%)
Gene names: GluA2, Glur2, Gria2
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand GOL 4 x GOL
Ligand SO4 4 x SO4
Ligand PVQ 1 x PVQ
Ligand NH4 1 x NH4
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: P21212
Unit cell:
a: 59.351Å b: 96.826Å c: 48.538Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.112 0.111 0.14
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects.
Golubeva et al. (2022)