› 5kcj

X-ray diffraction
2.09Å resolution

Structure of the human GluN1/GluN2A LBD in complex with GNE6901

Released:
DOI: 10.2210/pdb5kcj/pdb
PDB entry 5kcj coloured by chain, front view.
PDB entry 5kcj coloured by chain, side view.
PDB entry 5kcj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit Function.
Hackos DH, Lupardus PJ, Grand T, Chen Y, Wang TM, Reynen P, Gustafson A, Wallweber HJ, Volgraf M, Sellers BD, Schwarz JB, Paoletti P, Sheng M, Zhou Q, Hanson JE
Neuron 89 983-99 (2016)
PMID: 26875626

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-170222 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glutamate receptor ionotropic, NMDA 2A Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 31.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12879 (Residues: 401-539, 661-802; Coverage: 20%)
Gene names: GRIN2A, NMDAR2A
Sequence domains:
Structure domains: Periplasmic binding protein-like II
Glutamate receptor ionotropic, NMDA 1 Chain: B
Molecule details ›
Chain: B
Length: 293 amino acids
Theoretical weight: 33.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q05586 (Residues: 394-544, 663-800; Coverage: 31%)
Gene names: GRIN1, NMDAR1
Sequence domains:
Structure domains: Periplasmic binding protein-like II

Ligands and Environments

4 bound ligands:
Ligand ACT 1 x ACT
Ligand GLU 1 x GLU
Ligand GLY 1 x GLY
Ligand 6RM 1 x 6RM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P212121
Unit cell:
a: 54.41Å b: 89.73Å c: 124.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.225
Expression system: Escherichia coli

Quick links

Citations

26 review citations

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.
Wagner et al. (2016)
25 more

3 mentions without citation

The pathogenic S688Y mutation in the ligand-binding domain of the GluN1 subunit regulates the properties of NMDA receptors.
Skrenkova et al. (2020)
2 more