› 5b3j

X-ray diffraction
2.9Å resolution

Activation of NMDA receptors and the mechanism of inhibition by ifenprodil

Released:
DOI: 10.2210/pdb5b3j/pdb
PDB entry 5b3j coloured by chain, front view.
PDB entry 5b3j coloured by chain, side view.
PDB entry 5b3j coloured by chain, top view.
Source organisms:
Primary publication:
Activation of NMDA receptors and the mechanism of inhibition by ifenprodil.
Tajima N, Karakas E, Grant T, Simorowski N, Diaz-Avalos R, Grigorieff N, Furukawa H
Nature 534 63-8 (2016)
PMID: 27135925

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-103591 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Glutamate receptor ionotropic, NMDA 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 383 amino acids
Theoretical weight: 42.93 KDa
Source organism: Xenopus laevis
Expression system: Trichoplusia ni
UniProt:
  • Canonical: A0A1L8F5J9 (Residues: 23-190, 191-384; Coverage: 41%)
Gene name: grin1
Sequence domains: Receptor family ligand binding region
Structure domains: Rossmann fold
Glutamate receptor ionotropic, NMDA 2B Chains: C, D
Molecule details ›
Chains: C, D
Length: 364 amino acids
Theoretical weight: 41.37 KDa
Source organism: Rattus norvegicus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q00960 (Residues: 31-394; Coverage: 25%)
Gene name: Grin2b
Sequence domains: Receptor family ligand binding region
Structure domains: Rossmann fold
Fab, heavy chain Chains: E, H
Molecule details ›
Chains: E, H
Length: 224 amino acids
Theoretical weight: 23.91 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
Fab, light chain Chains: F, L
Molecule details ›
Chains: F, L
Length: 213 amino acids
Theoretical weight: 23.68 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: C2
Unit cell:
a: 247.249Å b: 79.903Å c: 181.314Å
α: 90° β: 127.09° γ: 90°
R-values:
R R work R free
0.275 0.273 0.302
Expression system: Trichoplusia ni

Quick links

Citations

27 review citations

Unravelling biological macromolecules with cryo-electron microscopy.
Fernandez-Leiro et al. (2016)
26 more

7 mentions without citation

Activation of NMDA receptors and the mechanism of inhibition by ifenprodil.
Tajima et al. (2016)
6 more