SMTL ID : 8e96.1

Glycine and glutamate bound Human GluN1a-GluN2D NMDA receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 6 residues within 4Å: Chain A: F.466, P.498, T.500, R.505, S.670, D.714 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.500, A:S.670, A:D.714 Salt bridges: A:R.505 GLY.5: 9 residues within 4Å: Chain C: F.466, P.498, L.499, T.500, R.505, S.669, S.670, W.713, D.714 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.670, C:D.714 Salt bridges: C:R.505

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

NAG.2: 2 residues within 4Å: Chain A: M.376, N.753 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain B: N.723 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain C: N.255, N.258, A.261 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.261 NAG.7: 5 residues within 4Å: Chain C: T.317, R.319, F.330, N.332, N.350 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain C: N.753 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain D: P.722, N.723 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.722 Hydrogen bonds: D:N.723

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.3: 11 residues within 4Å: Chain B: H.521, S.547, L.548, T.549, R.554, V.721, G.724, S.725, T.726, Y.766, D.767 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:S.547, B:T.549, B:S.725, B:T.726, B:D.767, E.3 Salt bridges: B:H.521, B:R.554 GLU.9: 9 residues within 4Å: Chain D: H.521, S.547, L.548, T.549, R.554, G.724, S.725, T.726, Y.766 9 PLIP interactions: 9 interactions with chain D, Hydrogen bonds: D:S.547, D:T.549, D:T.549, D:S.725, D:T.726, D:Y.766, D:Y.766 Salt bridges: D:H.521, D:R.554

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chou, T.H. et al., Structural insights into assembly and function of GluN1-2C, GluN1-2A-2C, and GluN1-2D NMDARs. Mol.Cell (2022)

Release Date

2022-12-07

Peptides

Glutamate receptor ionotropic, NMDA 1: AC
Glutamate receptor ionotropic, NMDA 2D: 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 2D