SMTL ID : 9iyq.1

Structure of the human GluN1-N2B NMDA receptors in the Mg2+ free state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.18 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 8 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.687, S.688, D.732 6 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain A Hydrogen bonds: G.1, G.1, A:P.516, A:T.518, A:S.688 Salt bridges: A:R.523 GLY.6: 9 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:P.516, C:P.516, C:T.518, C:S.688, G.6 Salt bridges: C:R.523

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

NAG.2: 3 residues within 4Å: Chain A: N.61, A.62, T.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.28 NAG.3: 4 residues within 4Å: Chain A: N.368, T.370, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: N.203, T.205, A.206 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain C: N.28, N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain C: N.276 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.276 NAG.9: 3 residues within 4Å: Chain C: N.368, T.370, I.373 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.368 NAG.10: 1 residues within 4Å: Chain C: N.471 No protein-ligand interaction detected (PLIP) NAG.11: 4 residues within 4Å: Chain C: M.394, P.767, W.768, N.771 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.768 Hydrogen bonds: C:P.767

2 x 7RC: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid(Covalent)(Non-covalent)

7RC.5: 10 residues within 4Å: Chain B: H.486, S.512, T.514, R.519, G.689, S.690, T.691, Y.731, D.732, Y.762 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.512, B:T.514, B:T.514, B:T.514, B:V.686, B:S.690, B:T.691 Salt bridges: B:H.486, B:R.519, B:D.732 7RC.12: 10 residues within 4Å: Chain D: H.486, S.512, T.514, R.519, G.689, S.690, T.691, Y.731, D.732, Y.762 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.512, D:T.514, D:T.514, D:S.690, D:T.691, D:T.691, D:T.691 Salt bridges: D:H.486, D:R.519, D:D.732

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, X. et al., Structural insights into the diverse actions of magnesium on NMDA receptors. Neuron (2025)

Release Date

2025-03-05

Peptides

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

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