SMTL ID : 9iyp.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.27 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 8 residues within 4Å: Chain A: F.458, P.490, L.491, T.492, R.497, S.661, S.662, D.706 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:T.492, A:S.662, A:D.706, G.1, G.1 Salt bridges: A:R.497 GLY.10: 9 residues within 4Å: Chain C: F.458, P.490, L.491, T.492, R.497, S.661, S.662, W.705, D.706 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.492, C:S.662, C:D.706 Salt bridges: C:R.497

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

NAG.2: 3 residues within 4Å: Chain A: N.342, T.344, H.345 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain C: N.177, T.179 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain C: N.250 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.250

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

7RC.3: 10 residues within 4Å: Chain B: H.452, S.478, T.480, R.485, G.655, S.656, T.657, Y.697, D.698, Y.728 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.478, B:T.480, B:T.480, B:S.656, B:T.657 Salt bridges: B:H.452, B:R.485, B:D.698 7RC.12: 9 residues within 4Å: Chain D: H.452, S.478, T.480, R.485, G.655, S.656, T.657, Y.697, Y.728 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.478, D:S.478, D:T.480, D:T.480, D:V.652, D:S.656, D:T.657, D:T.657, D:T.657 Salt bridges: D:H.452, D:R.485, D:D.698

7 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain B: D.102 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain B: D.320 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.320 MG.6: 1 residues within 4Å: Chain B: H.93 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: R.153, E.157 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: N.581, N.582 Chain C: N.590 Chain D: N.581 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain D: H.93 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain D: D.147 No protein-ligand interaction detected (PLIP)

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.
Show / Hide

Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2B