SMTL ID : 9d3a.1

Nonactive state of Gly-,Glu- bound GluN1a-2B-2D NMDAR (Low-res)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: P.745, N.749 No protein-ligand interaction detected (PLIP)

2 x GLY: GLYCINE(Non-covalent)

GLY.2: 6 residues within 4Å: Chain A: F.462, P.494, T.496, R.501, S.666, D.710 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.496, A:T.496, A:S.666 Salt bridges: A:R.501 GLY.6: 6 residues within 4Å: Chain C: F.462, P.494, T.496, R.501, S.666, D.710 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.666, C:D.710 Salt bridges: C:R.501

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.449 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.449 NAG.5: 1 residues within 4Å: Chain B: N.697 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain C: P.745, W.746, N.749 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.746 Hydrogen bonds: C:N.749 NAG.9: 2 residues within 4Å: Chain D: K.485, N.688 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.485

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 10 residues within 4Å: Chain B: H.495, S.521, T.523, R.528, V.695, G.698, S.699, T.700, Y.740, D.741 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:Y.740 Hydrogen bonds: B:S.521, B:T.523, B:T.523, B:S.699, B:T.700 Salt bridges: B:H.495, B:R.528 GLU.8: 10 residues within 4Å: Chain D: H.486, S.512, T.514, R.519, V.686, P.687, S.690, T.691, Y.731, D.732 8 PLIP interactions: 6 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:S.512, D:S.690, D:T.691, D:Y.731, E.8, E.8 Salt bridges: D:H.486, D:R.519

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, H. et al., Structural basis for channel gating and blockade in tri-heteromeric GluN1-2B-2D NMDA receptor. Neuron (2025)

Release Date

2025-02-26

Peptides

Glutamate receptor ionotropic, NMDA 1: AC
Glutamate receptor ionotropic, NMDA 2B: B
Glutamate receptor ionotropic, NMDA 2D: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2B

Glutamate receptor ionotropic, NMDA 2D

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