SMTL ID : 7saa.1

Glycine and glutamate bound GluN1a-GluN2B NMDA receptors in non-active 1 conformation at 2.97 Angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

3 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: P.718, N.719, R.743 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.368, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain D: K.516, V.717, N.719 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.203, T.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.203 NAG.5: 1 residues within 4Å: Chain A: N.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.276 NAG.6: 3 residues within 4Å: Chain A: N.368, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.522 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.522 NAG.10: 2 residues within 4Å: Chain C: N.203, T.205 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.203 NAG.11: 2 residues within 4Å: Chain C: N.276, A.279 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.276 NAG.13: 1 residues within 4Å: Chain D: N.522 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.522, D:N.522 NAG.14: 1 residues within 4Å: Chain D: N.372 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.372

2 x GLY: GLYCINE(Non-covalent)

GLY.7: 10 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732, F.758 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:P.516, A:P.516, A:T.518, A:S.688, G.7 Salt bridges: A:R.523 GLY.12: 9 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:P.516, C:P.516, C:T.518, C:S.688, G.12 Salt bridges: C:R.523

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.9: 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 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:Y.762 Hydrogen bonds: B:T.545, B:S.721, B:T.722, B:T.722 Salt bridges: B:H.517, B:R.550 GLU.15: 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 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:Y.762 Hydrogen bonds: D:T.545, D:S.721, D:T.722, D:T.722, D:Y.793, E.15, E.15 Salt bridges: D:H.517, D:R.550

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chou, T.H. et al., Structural insights into binding of therapeutic channel blockers in NMDA receptors. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-07-20

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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