SMTL ID : 7eor.1

Structure of the human GluN1/GluN2A NMDA receptor in the glycine/glutamate/GNE-6901 bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: K.487, P.686, N.687 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.686 Hydrogen bonds: A:K.487, A:N.687 NAG.3: 3 residues within 4Å: Chain B: N.28, N.61, T.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.61, B:T.63 NAG.4: 4 residues within 4Å: Chain B: N.273, N.276, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain B: M.237, N.239 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain B: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: P.767, W.768, N.771 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.767, B:N.771 NAG.8: 1 residues within 4Å: Chain B: N.471 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.471 NAG.9: 3 residues within 4Å: Chain C: K.487, P.686, N.687 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.686 Hydrogen bonds: C:K.487, C:N.687 NAG.11: 3 residues within 4Å: Chain D: N.28, N.61, T.63 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.61, D:T.63 NAG.12: 4 residues within 4Å: Chain D: N.273, N.276, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain D: M.237, N.239 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain D: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain D: P.767, W.768, N.771 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.767, D:N.771 NAG.16: 1 residues within 4Å: Chain D: N.471 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.471

2 x 6RM: 7-[(4-fluoranylphenoxy)methyl]-3-[(1~{R},2~{R})-2-(hydroxymethyl)cyclopropyl]-2-methyl-[1,3]thiazolo[3,2-a]pyrimidin-5-one(Non-covalent)

6RM.2: 18 residues within 4Å: Chain A: V.526, P.527, F.528, V.529, E.530, T.758, T.759, G.760, L.780, V.783 Chain B: I.519, K.531, P.532, F.533, Y.535, R.755, G.757, H.780 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.526, A:P.527, B:Y.535 Hydrogen bonds: A:E.530, A:T.758, B:G.757 6RM.10: 18 residues within 4Å: Chain C: V.526, P.527, F.528, V.529, E.530, T.758, T.759, G.760, L.780, V.783 Chain D: I.519, K.531, P.532, F.533, Y.535, R.755, G.757, H.780 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.526, C:P.527, D:Y.535 Hydrogen bonds: C:E.530, C:T.758, D:G.757

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Gating mechanism and a modulatory niche of human GluN1-GluN2A NMDA receptors. Neuron (2021)

Release Date

2021-06-30

Peptides

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

Glutamate receptor ionotropic, NMDA 1

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