SMTL ID : 9ooq.1

Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 9 residues within 4Å: Chain A: F.467, P.499, L.500, T.501, R.506, S.670, S.671, W.714, D.715 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:P.499, A:T.501, A:S.671, A:D.715, G.1 Salt bridges: A:R.506 GLY.9: 8 residues within 4Å: Chain C: F.467, P.499, L.500, T.501, R.506, S.671, W.714, D.715 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:P.499, C:P.499, C:T.501, C:S.671, G.9 Salt bridges: C:R.506

8 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.2: 18 residues within 4Å: Chain A: M.538, W.546, S.587, M.590, W.591, W.594, L.598, L.802, G.805, G.806, L.813 Chain D: T.635, I.639, S.642, V.643, F.646 Ligands: POV.3, POV.4 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:W.546, A:M.590, A:W.591, A:W.594, A:L.598, A:L.802, A:L.813, D:I.639, D:I.639, D:V.643, D:F.646 Hydrogen bonds: A:S.587, D:T.635, D:T.635 POV.3: 13 residues within 4Å: Chain A: M.538, S.543, W.546, L.547, V.549, G.550, W.594, L.597, I.626 Chain D: F.646, V.649 Ligands: POV.2, POV.4 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.546, A:W.546, A:V.549, A:W.594, A:L.597, A:I.626, D:F.646, D:V.649 Hydrogen bonds: A:S.543 POV.4: 11 residues within 4Å: Chain A: G.550, L.551, H.554, V.555, V.558, L.586, S.587, M.590, Y.820 Ligands: POV.2, POV.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.551, A:H.554, A:V.555, A:V.558, A:V.558, A:V.558, A:L.586 Hydrogen bonds: A:S.587, A:S.587, A:Y.820 POV.7: 14 residues within 4Å: Chain A: F.610, R.613, M.617, V.618 Chain B: T.610, I.611, G.612, I.615, W.616, W.619, F.623, M.833, L.840 Ligands: 01.6 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.615, B:W.616, B:W.619, B:F.623, B:L.840, A:F.610, A:F.610, A:V.618 POV.8: 19 residues within 4Å: Chain B: T.635, I.639, S.642, V.643, F.646 Chain C: M.538, W.546, S.587, M.590, W.591, W.594, L.598, M.801, L.802, G.805, G.806, L.813 Ligands: POV.10, POV.11 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:I.639, B:I.639, B:V.643, B:F.646, B:F.646, C:W.546, C:M.590, C:W.591, C:W.594, C:W.594, C:L.598, C:L.802 Hydrogen bonds: B:T.635 POV.10: 13 residues within 4Å: Chain B: F.646, V.649 Chain C: M.538, S.543, T.544, W.546, L.547, V.549, G.550, W.594, L.597 Ligands: POV.8, POV.11 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:F.646, B:V.649, C:W.546, C:L.547, C:V.549, C:L.597 Hydrogen bonds: C:S.543, C:T.544 POV.11: 10 residues within 4Å: Chain C: L.551, H.554, V.555, V.558, L.586, S.587, M.590, Y.820 Ligands: POV.8, POV.10 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:H.554, C:V.555, C:V.558, C:V.558, C:L.586 Hydrogen bonds: C:S.587, C:S.587, C:Y.820 POV.14: 15 residues within 4Å: Chain C: F.610, R.613, I.614, M.617, V.618 Chain D: T.610, I.611, G.612, I.615, W.616, W.619, F.623, M.833, L.840 Ligands: 01.13 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.615, D:W.616, D:W.619, D:F.623, D:L.840, C:F.610, C:F.610, C:I.614, C:V.618 Hydrogen bonds: D:T.610, D:I.611, D:G.612

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.5: 9 residues within 4Å: Chain B: H.495, S.521, L.522, T.523, R.528, S.699, T.700, Y.740, D.741 10 PLIP interactions: 1 Ligand-Ligand interactions, 9 interactions with chain B Hydrogen bonds: E.5, B:T.523, B:T.523, B:T.523, B:S.699, B:T.700, B:D.741 Hydrophobic interactions: B:Y.740 Salt bridges: B:H.495, B:R.528 GLU.12: 11 residues within 4Å: Chain D: H.495, S.521, L.522, T.523, R.528, V.695, G.698, S.699, T.700, Y.740, D.741 10 PLIP interactions: 9 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.740 Hydrogen bonds: D:T.523, D:V.695, D:S.699, D:T.700, D:D.741, D:D.741, E.12 Salt bridges: D:H.495, D:R.528

2 x 01: (10xi,13xi,24S)-14beta,17alpha-cholest-5-ene-3beta,24-diol

01.6: 11 residues within 4Å: Chain B: L.560, A.565, W.568, V.569, F.572, V.573, L.576, I.577, I.615, W.619 Ligands: POV.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.560, B:L.560, B:A.565, B:W.568, B:F.572, B:F.572, B:I.615 01.13: 11 residues within 4Å: Chain D: L.560, A.565, W.568, V.569, F.572, V.573, L.576, I.577, I.615, W.619 Ligands: POV.14 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.560, D:L.560, D:W.568, D:F.572, D:F.572, D:I.615, D:W.619, D:W.619

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hyunook, K. et al., Mechanism of conductance control and neurosteroid binding in NMDA receptors. Nature (2025)

Release Date

2025-10-29

Peptides

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

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

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