SMTL ID : 8hdk.1

Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (minor class in symmetry)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain A: N.276, S.278, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: I.26, N.28, N.61, A.62, T.63, S.85 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.61, A.62 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: N.276, S.278, A.279, S.282 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain D: N.685 No protein-ligand interaction detected (PLIP)

3 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.3: 2 residues within 4Å: Chain A: N.771, L.774 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 3 residues within 4Å: Chain B: G.481, P.684, N.685 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.7: 2 residues within 4Å: Chain C: W.768, N.771 No protein-ligand interaction detected (PLIP)

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

NAG.9: 4 residues within 4Å: Chain A: K.202, N.203, V.204, T.205 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.204 NAG.10: 3 residues within 4Å: Chain A: R.212, L.238, N.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.239 NAG.11: 5 residues within 4Å: Chain A: T.335, G.336, R.337, N.350 Ligands: NAG.12 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain A: I.366, N.368, H.371 Ligands: NAG.11 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain A: T.396, M.470, N.471 No protein-ligand interaction detected (PLIP) NAG.14: 4 residues within 4Å: Chain B: S.302, R.333, H.334, N.337 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:H.334 Hydrogen bonds: B:S.302, B:R.333, B:R.333 NAG.15: 4 residues within 4Å: Chain C: R.212, M.237, L.238, N.239 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.238 Hydrogen bonds: C:R.212 NAG.16: 7 residues within 4Å: Chain C: I.272, T.335, G.336, R.337, R.346, N.350, N.368 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain C: N.368, T.370, H.371, V.372, I.373 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.368, C:H.371, C:V.372 NAG.18: 3 residues within 4Å: Chain C: T.396, M.470, N.471 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.396 NAG.19: 2 residues within 4Å: Chain C: N.203, A.206 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain D: R.333, N.337 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.306, D:N.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-03-29

Peptides

Glutamate receptor ionotropic, NMDA 1: AC
Glutamate receptor ionotropic, NMDA 2C: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2C

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