SMTL ID : 9oot.1

Pre-active state of Gly/Glu/Pregnenolone Sulfate bound hGluN1a-2B NMDAR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.13 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.7: 9 residues within 4Å: Chain C: 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 C, 1 Ligand-Ligand interactions Hydrogen bonds: C:P.499, C:T.501, C:S.671, C:D.715, G.7 Salt bridges: C:R.506

4 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: F.537, M.538, S.587, W.591, W.594, L.598, L.802, G.805, A.809, L.813 Chain D: T.635, S.642, V.643, F.646 Ligands: POV.3 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.537, A:W.591, A:W.594, A:L.598, A:L.802, A:A.809, A:L.813, D:V.643, D:F.646, D:F.646 POV.3: 12 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 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.546, A:L.547, A:V.549, A:W.594, A:L.597, A:I.626, D:F.646, D:V.649 POV.8: 12 residues within 4Å: Chain B: T.635, I.639, S.642, V.643, F.646 Chain C: F.537, M.538, S.587, W.591, L.598, L.802 Ligands: POV.9 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:F.537, C:W.591, C:L.598, C:L.802, B:I.639, B:V.643, B:F.646, B:F.646 Hydrogen bonds: B:T.635 POV.9: 11 residues within 4Å: Chain B: F.646, V.649 Chain C: M.538, S.543, W.546, L.547, V.549, G.550, L.597, I.626 Ligands: POV.8 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:F.646, B:V.649, C:W.546, C:W.546, C:W.546, C:L.547, C:V.549, C:L.597, C:L.597, C:I.626

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 11 residues within 4Å: Chain B: H.495, S.521, L.522, T.523, R.528, V.695, G.698, S.699, T.700, Y.740, D.741 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.740 Hydrogen bonds: B:T.523, B:T.523, B:T.523, B:V.695, B:S.699, B:T.700, E.4 Salt bridges: B:K.494, B:H.495, B:R.528 GLU.10: 12 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, Y.771 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:T.700, D:Y.740 Hydrogen bonds: D:T.523, D:T.523, D:S.699, D:S.699, D:T.700, D:T.700, D:E.701, D:Y.740, D:D.741 Salt bridges: D:H.495, D:R.528

4 x A8W: Pregnenolone sulfate(Non-covalent)

A8W.5: 12 residues within 4Å: Chain A: M.617, V.618, G.621, I.625 Chain B: L.560, A.565, W.568, F.572, W.619, F.623, M.833 Ligands: A8W.6 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.560, B:W.568, B:W.568, B:W.568, B:F.572, B:W.619, B:F.623, A:I.625 A8W.6: 6 residues within 4Å: Chain B: G.829, Y.832, M.833, A.836, A.837 Ligands: A8W.5 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.833, B:A.836 A8W.11: 11 residues within 4Å: Chain C: M.617, V.618, G.621, I.625 Chain D: L.560, W.568, F.572, W.619, F.623, M.833 Ligands: A8W.12 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.560, D:W.568, D:W.568, D:W.568, D:F.572, D:W.619, D:F.623, C:I.625 A8W.12: 6 residues within 4Å: Chain D: G.829, Y.832, M.833, A.836, A.837 Ligands: A8W.11 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:M.833, D:A.836

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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