SMTL ID : 7eou.1

Structure of the human GluN1/GluN2A NMDA receptor in the glycine/glutamate/GNE-6901/9-AA bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: K.484, P.686, N.687, Q.710, K.711 Ligand excluded by PLIP NAG.3: 5 residues within 4Å: Chain B: N.28, R.43, N.61, A.62, T.63 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain B: N.203, T.205 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain B: M.237, N.239 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain B: N.273, N.276 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain B: N.350, I.366, N.368 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain B: N.471 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain B: P.767, W.768, N.771 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain C: K.484, P.686, N.687, Q.710, K.711 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain D: N.28, R.43, N.61, A.62, T.63 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: N.203, T.205 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain D: M.237, N.239 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: N.273, N.276 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain D: N.350, I.366, N.368 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain D: N.471 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: P.767, W.768, N.771 Ligand excluded by PLIP

1 x AA: 9-AMINOACRIDINE(Non-functional Binders)

AA.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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.10: 21 residues within 4Å: Chain A: I.514, 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, K.534, Y.535, R.755, G.757, L.777, H.780 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.526, A:P.527, B:P.532, B:Y.535 6RM.12: 18 residues within 4Å: Chain C: I.514, V.526, P.527, F.528, V.529, E.530, T.758, T.759, G.760, V.783 Chain D: I.519, P.532, F.533, Y.535, R.755, G.757, L.777, H.780 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:P.532, D:Y.535, C:V.526, C:P.527 pi-Stacking: D:Y.535

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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