SMTL ID : 9d39.1

Gly-,PPDA- bound GluN1a-2B-2D NMDAR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 7 residues within 4Å: Chain A: F.462, P.494, L.495, T.496, W.709, D.710, F.736 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.496, A:D.710 GLY.5: 7 residues within 4Å: Chain C: F.462, P.494, T.496, R.501, S.666, W.709, D.710 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.496, C:S.666, C:D.710 Salt bridges: C:R.501

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

NAG.2: 3 residues within 4Å: Chain A: P.745, W.746, N.749 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.746 Hydrogen bonds: A:N.749 NAG.3: 1 residues within 4Å: Chain A: N.449 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain C: M.372, P.745, N.749 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.745

2 x 2JL: (2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid(Non-covalent)

2JL.4: 13 residues within 4Å: Chain B: A.423, K.494, H.495, S.521, L.522, T.523, R.528, S.699, V.723, Y.740, V.744, Y.747, Y.771 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:A.423, B:V.723, B:Y.740, B:V.744, B:Y.747 Hydrogen bonds: B:K.494, B:S.521, B:S.521, B:T.523, B:T.523, B:T.523, B:S.699, B:S.699 Salt bridges: B:H.495, B:R.528 2JL.7: 14 residues within 4Å: Chain D: E.412, R.413, P.414, H.486, S.512, T.514, R.519, S.690, V.714, Y.731, D.732, V.735, M.739, Y.762 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:E.412, D:R.413, D:Y.731, D:V.735 Hydrogen bonds: D:S.512, D:T.514, D:T.514, D:S.690, D:S.690 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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