SMTL ID : 9oor.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.15 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.8: 8 residues within 4Å: Chain C: F.467, P.499, T.501, R.506, S.670, S.671, W.714, D.715 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.501, C:T.501, C:S.671, C:S.671 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: 15 residues within 4Å: Chain A: M.538, L.551, H.554, L.586, S.587, M.590, W.591, W.594, L.802 Chain D: T.635, I.639, S.642, V.643 Ligands: POV.3, POV.4 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:I.639, D:V.643, A:L.551, A:W.594, A:L.802 Hydrogen bonds: D:T.635, A:S.587 POV.3: 10 residues within 4Å: Chain A: L.534, D.535, F.537, G.798, M.801, L.802, G.805, A.809 Ligands: POV.2, POV.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.534, A:F.537, A:A.809 POV.4: 17 residues within 4Å: Chain A: D.535, M.538, Q.539, Q.542, S.543, W.546, L.547, V.549, G.550, W.594, L.598, I.626, V.627 Chain B: Q.821 Chain D: F.646 Ligands: POV.2, POV.3 11 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 9 interactions with chain A Hydrogen bonds: B:Q.821, A:Q.539, A:Q.542, A:S.543 Hydrophobic interactions: D:F.646, A:W.546, A:L.547, A:V.549, A:W.594, A:I.626, A:V.627 POV.7: 16 residues within 4Å: Chain A: F.610, R.613, M.617, V.618, M.624, I.625 Chain B: W.568, T.610, I.611, G.612, K.613, I.615, W.619, F.623, L.840 Ligands: 01.6 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.568, B:W.568, B:I.615, B:I.615, B:W.619, B:F.623, B:L.840, A:F.610, A:F.610, A:M.617, A:I.625 Hydrogen bonds: B:T.610, B:G.612 Salt bridges: A:R.613 POV.9: 17 residues within 4Å: Chain B: T.635, I.639, S.642, V.643, F.646 Chain C: G.550, L.551, H.554, L.586, S.587, M.590, W.591, W.594, L.598, L.802 Ligands: POV.10, POV.11 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.594, C:W.594, C:L.598, B:I.639, B:V.643 Hydrogen bonds: B:T.635 POV.10: 10 residues within 4Å: Chain C: L.534, D.535, F.537, M.801, L.802, G.805, V.808, A.809 Ligands: POV.9, POV.11 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.537, C:V.808, C:A.809 POV.11: 13 residues within 4Å: Chain B: F.646 Chain C: D.535, M.538, S.543, W.546, L.547, V.549, L.597, L.598, V.627, Y.630 Ligands: POV.9, POV.10 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:D.535, C:V.549, C:L.597, C:L.598, C:V.627, C:Y.630, B:F.646 Hydrogen bonds: C:S.543 POV.12: 16 residues within 4Å: Chain C: F.610, R.613, M.617, V.618, I.625 Chain D: W.568, T.610, I.611, G.612, I.615, W.616, W.619, F.623, Y.655, M.833, L.840 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:W.568, D:W.568, D:I.615, D:I.615, D:W.616, D:W.619, D:F.623, D:L.840, C:F.610, C:M.617, C:V.618, C:I.625 Hydrogen bonds: D:G.612 Salt bridges: D:K.613, C:R.613

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: 10 interactions with chain B, Hydrophobic interactions: B:Y.740 Hydrogen bonds: B:T.523, B:V.695, B:S.699, B:S.699, B:T.700, B:T.700, B:D.741 Salt bridges: B:H.495, B:R.528 GLU.13: 9 residues within 4Å: Chain D: H.495, S.521, L.522, T.523, R.528, 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:S.699, D:S.699, D:T.700, D:D.741, D:D.741, E.13 Salt bridges: D:H.495, D:R.528

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

01.6: 9 residues within 4Å: Chain B: L.560, A.565, W.568, F.572, V.573, I.577, I.615, W.619 Ligands: POV.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.560, B:W.568, B:W.568, B:F.572, B:F.572, B:V.573, B:I.577, B:I.615 Hydrogen bonds: B:W.619 01.14: 7 residues within 4Å: Chain D: L.560, W.568, F.572, V.573, I.577, I.615, W.619 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.560, D:W.568, D:W.568, D:F.572, D:F.572, D:V.573, D:I.577, D:I.615 Hydrogen bonds: 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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