SMTL ID : 9c7e.1

Diheteromeric GluN1/GluN2A (delM653) in nanodisc complex with glycine, glutamate, and GNE-4123, open conformation, C2 symmetry

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x 01: 4-cyclohexyl-N-[(8R)-2-cyclopropyl-7-hydroxy-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]benzene-1-sulfonamide

01.1: 4 residues within 4Å: Chain A: T.550, L.551, D.552, G.815 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.551, A:D.552 Hydrogen bonds: A:L.551, A:D.552 01.6: 2 residues within 4Å: Chain C: L.551, D.552 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.551, C:D.552 Hydrogen bonds: C:L.551, C:D.552

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 7 residues within 4Å: Chain A: V.635 Chain B: P.546, S.547, M.822, A.825 Ligands: Y01.3, D12.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.546, B:A.825, A:V.635 Y01.3: 11 residues within 4Å: Chain B: S.547, L.550, A.555, W.558, V.559, F.562, V.563, I.567, W.609 Ligands: Y01.2, D12.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.550, B:L.550, B:A.555, B:W.558, B:V.559, B:F.562, B:V.563, B:I.567 Hydrogen bonds: B:S.547 Y01.5: 8 residues within 4Å: Chain A: L.565 Chain B: I.813, D.814, A.817, F.820, Y.821, A.824, M.827 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.813, B:Y.821, B:A.824, B:M.827, A:L.565, A:L.565 Y01.7: 7 residues within 4Å: Chain C: V.635 Chain D: P.546, S.547, M.822, A.825 Ligands: Y01.8, D12.9 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:P.546, D:A.825, C:V.635 Y01.8: 11 residues within 4Å: Chain D: S.547, L.550, A.555, W.558, V.559, F.562, V.563, I.567, W.609 Ligands: Y01.7, D12.9 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.550, D:L.550, D:A.555, D:W.558, D:V.559, D:V.563, D:I.567 Hydrogen bonds: D:S.547 Y01.10: 8 residues within 4Å: Chain C: L.565 Chain D: I.813, D.814, F.820, Y.821, L.823, A.824, M.827 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.813, D:Y.821, D:L.823, C:L.565

2 x D12: DODECANE(Non-covalent)

D12.4: 7 residues within 4Å: Chain A: I.631, M.634, V.635 Chain B: G.602, W.609 Ligands: Y01.2, Y01.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.631, A:V.635, B:W.609 D12.9: 8 residues within 4Å: Chain C: I.631, M.634, V.635 Chain D: G.602, I.605, W.609 Ligands: Y01.7, Y01.8 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.631, C:M.634, C:V.635, D:I.605, D:W.609, D:W.609

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jalali-Yazdi, F. et al., Diheteromeric GluN1/GluN2A (delM653) in nanodisc complexed with glycine, glutamate, and GNE-4123, open-pore conformation, processed in C2 symmetry. To Be Published

Release Date

2025-09-24

Peptides

Glutamate receptor ionotropic, NMDA 1,Green fluorescent protein chimera: AC
Glutamate receptor ionotropic, NMDA 2A,Green fluorescent protein chimera: 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,Green fluorescent protein chimera

Glutamate receptor ionotropic, NMDA 2A,Green fluorescent protein chimera

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