SMTL ID : 9oou.1

Glycine/Glutamate/EU 1622-240 rGluN1a-2B NMDAR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.34 Å

Oligo State

hetero-2-2-mer

Ligands

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

POV.1: 14 residues within 4Å: Chain A: S.553, M.555, S.560, W.563, L.564, G.567, W.608, W.611, L.614, L.615, V.644 Chain D: I.640, F.647 Ligands: 01.2 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:W.563, A:W.563, A:W.563, A:W.563, A:L.564, A:W.608, A:L.614, A:L.615, A:V.644, D:I.640, D:F.647, D:F.647, D:F.647 Hydrogen bonds: A:S.553 POV.5: 15 residues within 4Å: Chain B: I.640, F.647 Chain C: S.553, M.555, S.560, W.563, L.564, G.567, W.608, W.611, L.614, L.615, V.644, Y.647 Ligands: 01.6 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:I.640, B:F.647, B:F.647, B:F.647, C:W.563, C:W.563, C:W.563, C:W.563, C:L.564, C:W.608, C:L.614, C:L.615, C:V.644 Hydrogen bonds: C:S.553

4 x 01: (5M)-5-(3-bromo-4-fluorophenyl)-6-ethynyl-3-[2-(3-fluoro-3-methylazetidin-1-yl)-2-oxoethyl]thieno[2,3-d]pyrimidin-4(3H)-one

01.2: 15 residues within 4Å: Chain A: L.551, D.552, S.553, F.554, M.555, L.651, E.811, N.812, M.813, A.814, G.815, V.816, M.818 Chain D: S.655 Ligands: POV.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.554 Hydrogen bonds: A:F.554, A:G.815, A:V.816 01.3: 8 residues within 4Å: Chain B: S.558, L.561, A.566, V.570, F.573, W.620, M.834 Ligands: CLR.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.561, B:F.573, B:W.620 01.6: 14 residues within 4Å: Chain B: S.655 Chain C: L.551, D.552, S.553, F.554, L.651, E.811, N.812, M.813, A.814, G.815, V.816, M.818 Ligands: POV.5 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.554 Hydrogen bonds: C:F.554, C:G.815, C:V.816 01.7: 8 residues within 4Å: Chain D: S.558, L.561, W.569, V.570, F.573, W.620, M.834 Ligands: CLR.8 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.561, D:F.573, D:W.620

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 7 residues within 4Å: Chain B: P.557, S.558, L.561, Y.833, M.834, L.841 Ligands: 01.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.557, B:L.561, B:Y.833, B:Y.833, B:L.841 CLR.8: 8 residues within 4Å: Chain C: V.635 Chain D: P.557, S.558, L.561, Y.833, A.837, L.841 Ligands: 01.7 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.833, D:L.841, C:V.635

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, H. 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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