› 5ewl

X-ray diffraction
2.98Å resolution

CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH MK-22

Released:
DOI: 10.2210/pdb5ewl/pdb
PDB entry 5ewl coloured by chain, front view.
PDB entry 5ewl coloured by chain, side view.
PDB entry 5ewl coloured by chain, top view.
Source organisms:
Primary publication:
A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists.
Stroebel D, Buhl DL, Knafels JD, Chanda PK, Green M, Sciabola S, Mony L, Paoletti P, Pandit J
Mol Pharmacol 89 541-51 (2016)
PMID: 26912815

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-103593 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Glutamate receptor ionotropic, NMDA 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 390 amino acids
Theoretical weight: 43.76 KDa
Source organism: Xenopus laevis
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: A0A1L8F5J9 (Residues: 23-190, 191-387; Coverage: 41%)
Gene name: grin1
Sequence domains: Receptor family ligand binding region
Structure domains: Rossmann fold
Glutamate receptor ionotropic, NMDA 2B Chains: B, D
Molecule details ›
Chains: B, D
Length: 364 amino acids
Theoretical weight: 41.35 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13224 (Residues: 31-394; Coverage: 25%)
Gene names: GRIN2B, NMDAR2B
Sequence domains: Receptor family ligand binding region
Structure domains: Rossmann fold

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand NA 6 x NA
Ligand NAG 6 x NAG
Ligand 5SL 2 x 5SL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: C2
Unit cell:
a: 268.88Å b: 59.94Å c: 144.45Å
α: 90° β: 116.51° γ: 90°
R-values:
R R work R free
0.164 0.162 0.217
Expression system: Spodoptera frugiperda

Quick links

Citations

10 review citations

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

3 mentions without citation

A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists.
Stroebel et al. (2016)
2 more