SMTL ID : 9arf.1

Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in nonactive1 conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain B: V.717, P.718, N.719 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain D: V.717, P.718, N.719 No protein-ligand interaction detected (PLIP)

2 x GLY: GLYCINE(Non-covalent)

GLY.3: 9 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.516, A:T.518, A:S.688 Salt bridges: A:R.523 GLY.6: 9 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.516, C:T.518, C:S.688 Salt bridges: C:R.523

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 1 residues within 4Å: Chain B: N.522 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain D: N.522 No protein-ligand interaction detected (PLIP)

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.5: 10 residues within 4Å: Chain B: H.517, S.543, L.544, T.545, R.550, G.720, S.721, T.722, Y.762, D.763 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.762 Hydrogen bonds: B:S.543, B:S.721, B:T.722, B:D.763, E.5 Salt bridges: B:H.517, B:R.550 GLU.8: 10 residues within 4Å: Chain D: H.517, S.543, L.544, T.545, R.550, G.720, S.721, T.722, Y.762, D.763 8 PLIP interactions: 7 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.762 Hydrogen bonds: D:S.543, D:S.721, D:T.722, D:D.763, E.8 Salt bridges: D:H.517, D:R.550

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chou, T.H. et al., Molecular mechanism of ligand gating and opening of NMDA receptor. Nature (2024)

Release Date

2024-07-31

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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