SMTL ID : 7yfl.1

Structure of GluN1a-GluN2D NMDA receptor in complex with agonists glycine and glutamate.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

4 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: 4 residues within 4Å: Chain A: M.394, P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: K.512, K.515, N.715, Q.738 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: K.512, K.515, N.715, Q.738 No protein-ligand interaction detected (PLIP)

2 x GLY: GLYCINE(Non-covalent)

GLY.5: 8 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.688, W.731, F.758 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.12: 8 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.688, W.731, F.758 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.516, C:T.518, C:S.688 Salt bridges: C:R.523

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

NAG.6: 2 residues within 4Å: Chain A: N.61, T.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.61 NAG.7: 2 residues within 4Å: Chain A: T.396, N.471 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.440, H.449 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.440 NAG.9: 3 residues within 4Å: Chain A: G.336, N.350, N.368 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.350 Hydrogen bonds: A:N.350, A:N.350 NAG.10: 3 residues within 4Å: Chain A: N.203, T.205, A.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.206 NAG.13: 3 residues within 4Å: Chain C: N.203, T.205, A.206 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.206 NAG.14: 3 residues within 4Å: Chain C: G.336, N.350, N.368 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.350 Hydrogen bonds: C:N.350, C:N.350 NAG.15: 2 residues within 4Å: Chain C: N.440, D.441 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.441 NAG.16: 3 residues within 4Å: Chain C: N.61, S.84, S.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.61 NAG.17: 2 residues within 4Å: Chain C: T.396, N.471 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.396

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.11: 10 residues within 4Å: Chain B: H.513, T.541, R.546, N.715, G.716, S.717, T.718, Y.758, D.759, Y.789 10 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.758 Hydrogen bonds: B:T.541, B:S.717, B:T.718, B:D.759, E.11, E.11 Salt bridges: B:H.513, B:H.513, B:R.546 GLU.18: 10 residues within 4Å: Chain D: H.513, T.541, R.546, N.715, G.716, S.717, T.718, Y.758, D.759, Y.789 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:Y.758 Hydrogen bonds: D:T.541, D:S.717, D:T.718, D:D.759, E.18, E.18 Salt bridges: D:H.513, D:H.513, D:R.546

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-04-12

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

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