SMTL ID : 7yff.1

Structure of GluN1a-GluN2D NMDA receptor in complex with agonist glycine and competitive antagonist CPP.

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: 7 residues within 4Å: Chain A: V.46, N.61, A.62, T.63, S.84, S.85, R.306 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain C: N.771 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: N.471, F.472, T.473 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.471 Hydrogen bonds: A:N.471 NAG.5: 3 residues within 4Å: Chain A: K.275, N.276, A.279 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.279 Hydrogen bonds: A:K.275 NAG.7: 3 residues within 4Å: Chain A: N.368, T.370, H.371 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.371 NAG.9: 1 residues within 4Å: Chain C: N.471 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain C: N.276, A.279, T.335 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.276 NAG.11: 2 residues within 4Å: Chain C: Q.59, N.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.61 NAG.13: 3 residues within 4Å: Chain C: N.368, T.370, H.371 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.370, C:H.371

2 x GLY: GLYCINE(Non-covalent)

GLY.6: 8 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.687, S.688, 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.12: 8 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.687, S.688, 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 7RC: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid(Covalent)

7RC.8: 12 residues within 4Å: Chain B: H.513, S.539, L.540, T.541, R.546, V.713, G.716, S.717, T.718, Y.758, D.759, Y.789 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.539, B:S.539, B:T.541, B:Y.758, B:Y.789 Salt bridges: B:H.513, B:R.546 7RC.14: 12 residues within 4Å: Chain D: H.513, S.539, L.540, T.541, R.546, V.713, G.716, S.717, T.718, Y.758, D.759, Y.789 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.539, D:S.539, D:T.541, D:Y.758, D:Y.789 Salt bridges: 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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