› 3gba

X-ray diffraction
1.35Å resolution

X-ray structure of iGluR5 ligand-binding core (S1S2) in complex with dysiherbaine at 1.35A resolution

Released:
DOI: 10.2210/pdb3gba/pdb
PDB entry 3gba coloured by chain, front view.
PDB entry 3gba coloured by chain, side view.
PDB entry 3gba coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Full domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high affinity agonist dysiherbaine and the functional antagonist 8,9-dideoxyneodysiherbaine.
Frydenvang K, Lash LL, Naur P, Postila PA, Pickering DS, Smith CM, Gajhede M, Sasaki M, Sakai R, Pentikaïnen OT, Swanson GT, Kastrup JS
J Biol Chem 284 14219-29 (2009)
PMID: 19297335

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149793 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glutamate receptor ionotropic, kainate 1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 257 amino acids
Theoretical weight: 29.11 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P22756 (Residues: 445-559, 682-820; Coverage: 28%)
Gene names: Glur5, Grik1
Sequence domains:
Structure domains: Periplasmic binding protein-like II

Ligands and Environments

4 bound ligands:
Ligand DYH 4 x DYH
Ligand SO4 2 x SO4
Ligand GOL 3 x GOL
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-2
Spacegroup: P1
Unit cell:
a: 44.872Å b: 66.902Å c: 90.342Å
α: 92.69° β: 94.66° γ: 100.82°
R-values:
R R work R free
0.165 0.165 0.193
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Glutamate receptor ion channels: structure, regulation, and function.
Traynelis et al. (2010)
9 more

4 mentions without citation

Ligand pose and orientational sampling in molecular docking.
Coleman et al. (2013)
3 more