SMTL ID : 8xlk.1

Structure of native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat cortex and hippocampus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-2-2-1-1-1-1-mer

Ligands

2 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 3 residues within 4Å: Chain A: P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 4 residues within 4Å: Chain C: P.767, W.768, N.771 Chain H: A.27 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain B: N.687, R.711 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.61, T.63 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.203, A.206 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.239 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.276, A.279 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.300 Ligand excluded by PLIP NAG.9: 6 residues within 4Å: Chain A: I.272, T.335, G.336, R.337, N.350, N.368 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: T.396, N.471 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain B: N.541 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: S.305, E.308, N.340 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.380 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain C: I.26, N.28, Q.59, N.61, T.63 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain C: K.202, N.203, V.204, T.205, A.206 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: M.237, L.238, N.239 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain C: N.276, S.278, A.279 Chain I: Y.49 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.300 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain C: I.272, N.273, T.335, G.336, R.337, N.350 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.471 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain D: N.542 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: N.341, N.348 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.688, R.712 Ligand excluded by PLIP

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

7RC.14: 11 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, Y.761 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.730, B:D.731 Hydrogen bonds: B:S.511, B:S.511, B:T.513, B:S.689, B:Y.761 Salt bridges: B:H.485, B:R.518, B:D.731 7RC.25: 11 residues within 4Å: Chain D: H.486, S.512, L.513, T.514, R.519, G.689, S.690, T.691, Y.731, D.732, Y.762 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.731 Hydrogen bonds: D:S.512, D:S.512, D:T.514, D:G.689, D:S.690, D:T.691, D:Y.762 Salt bridges: D:H.486, D:R.519, D:D.732

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, M. et al., Assembly and architecture of endogenous NMDA receptors in adult cerebral cortex and hippocampus. Cell (2025)

Release Date

2025-02-05

Peptides

Glutamate receptor ionotropic, NMDA 1: AC
Glutamate receptor ionotropic, NMDA 2A: B
Glutamate receptor ionotropic, NMDA 2B: D
Heavy Chain of GluN1 Fab, 4F11: EI
Light Chain of GluN1 Fab, 4F11: FJ
Heavy Chain of GluN2A Fab, 28C: G
Light Chain of GluN2A Fab, 28C: H
Heavy Chain of GluN2B Fab2: K
Light Chain of GluN2B Fab2: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

I
I

F
F

J
J

G
G

H
H

K
K

L
L

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2A

Glutamate receptor ionotropic, NMDA 2B

Heavy Chain of GluN1 Fab, 4F11

Light Chain of GluN1 Fab, 4F11

Heavy Chain of GluN2A Fab, 28C

Light Chain of GluN2A Fab, 28C

Heavy Chain of GluN2B Fab2

Light Chain of GluN2B Fab2