› 5dex

X-ray diffraction
2.4Å resolution

Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, phenyl-ACEPC

Released:
DOI: 10.2210/pdb5dex/pdb
PDB entry 5dex coloured by chain, front view.
PDB entry 5dex coloured by chain, side view.
PDB entry 5dex coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.
Lind GE, Mou TC, Tamborini L, Pomper MG, De Micheli C, Conti P, Pinto A, Hansen KB
Proc Natl Acad Sci U S A 114 E6942-E6951 (2017)
PMID: 28760974

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152907 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glutamate receptor ionotropic, NMDA 1 Chain: A
Molecule details ›
Chain: A
Length: 292 amino acids
Theoretical weight: 33.34 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P35439 (Residues: 394-544, 663-800; Coverage: 31%)
Gene names: Grin1, Nmdar1
Sequence domains:
Structure domains: Periplasmic binding protein-like II
Glutamate receptor ionotropic, NMDA 2A Chain: B
Molecule details ›
Chain: B
Length: 283 amino acids
Theoretical weight: 31.79 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00959 (Residues: 402-539, 661-802; Coverage: 19%)
Gene name: Grin2a
Sequence domains:
Structure domains: Periplasmic binding protein-like II

Ligands and Environments

2 bound ligands:
Ligand GLY 1 x GLY
Ligand 5E0 1 x 5E0
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 54.629Å b: 87.302Å c: 122.572Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.207 0.285
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Structure, function, and allosteric modulation of NMDA receptors.
Hansen et al. (2018)
7 more

1 mention without citation

Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.
Lind et al. (2017)