SMTL ID : 7eu7.1

Structure of the human GluN1-GluN2A NMDA receptor in complex with S-ketamine, glycine and glutamate

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: I.26, N.61, A.62, T.63 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.203, T.205, A.206 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.239 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.276, A.279, V.334 Ligand excluded by PLIP NAG.5: 6 residues within 4Å: Chain A: T.335, G.336, R.337, R.346, F.348, N.350 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.368, G.369, H.371, I.373 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.440, D.441, P.447, H.449 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.471 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: P.767, W.768, N.771 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: N.340, T.342 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain B: N.380 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: V.489, P.686, N.687 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain C: I.26, N.61, A.62 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain C: N.203, T.205, A.206 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain C: N.239 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: N.276, A.279, V.334 Ligand excluded by PLIP NAG.19: 6 residues within 4Å: Chain C: T.335, G.336, R.337, R.346, F.348, N.350 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.368, G.369, I.373 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.440, D.441, H.449 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.471 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: P.767, W.768, N.771 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain D: N.340 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.380, H.381 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: K.487, N.687 Ligand excluded by PLIP

2 x GLY: GLYCINE(Non-covalent)

GLY.10: 9 residues within 4Å: Chain A: F.484, P.516, T.518, R.523, S.687, S.688, W.731, D.732, F.758 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.516, A:T.518, A:R.523, A:S.688 GLY.24: 8 residues within 4Å: Chain C: F.484, P.516, T.518, R.523, S.687, S.688, W.731, F.758 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.516, C:T.518, C:R.523, C:S.688

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.14: 10 residues within 4Å: Chain B: H.485, S.511, L.512, T.513, R.518, G.688, S.689, T.690, Y.730, D.731 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:Y.730 Hydrogen bonds: B:T.513, B:T.513, B:R.518, B:S.689, B:T.690, B:D.731 GLU.28: 10 residues within 4Å: Chain D: H.485, S.511, L.512, T.513, R.518, G.688, S.689, T.690, Y.730, D.731 8 PLIP interactions: 8 interactions with chain D, Hydrophobic interactions: D:Y.730 Hydrogen bonds: D:T.513, D:T.513, D:R.518, D:R.518, D:S.689, D:T.690, D:D.731

1 x JC9: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one(Non-covalent)

JC9.29: 3 residues within 4Å: Chain B: L.642 Chain D: L.642, T.646 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.642, D:T.646, B:L.642

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Structural basis of ketamine action on human NMDA receptors. Nature (2021)

Release Date

2021-08-04

Peptides

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

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