SMTL ID : 7yfh.1

Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

5 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: 2 residues within 4Å: Chain A: W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.2: 2 residues within 4Å: Chain A: N.276, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 4 residues within 4Å: Chain A: N.368, H.371, I.373 Chain D: Q.395 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.395, D:Q.395 NAG-NAG-MAN.8: 4 residues within 4Å: Chain B: K.485, P.684, N.685, R.709 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 3 residues within 4Å: Chain C: N.276, A.279, V.334 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 3 residues within 4Å: Chain A: I.26, N.61, A.62 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: G.336, R.337, F.348, N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.471 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: Q.306, R.333, H.334, N.337 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.471 Ligands: NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.368, T.370, H.371 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: I.26, N.28, N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: M.394, P.767, W.768, N.771 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain D: K.482, N.685 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain D: Q.306, Y.307, H.334, N.337 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.306

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

NAG.18: 2 residues within 4Å: Chain A: R.212, N.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.212, A:R.212 NAG.19: 1 residues within 4Å: Chain A: N.300 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain A: N.491, N.492 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain A: N.440, P.447 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.447 NAG.23: 3 residues within 4Å: Chain B: N.438, F.441, L.446 No protein-ligand interaction detected (PLIP) NAG.24: 1 residues within 4Å: Chain B: N.70 No protein-ligand interaction detected (PLIP) NAG.27: 1 residues within 4Å: Chain C: N.491 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.491 NAG.28: 5 residues within 4Å: Chain C: T.335, G.336, F.348, N.350, N.368 No protein-ligand interaction detected (PLIP) NAG.29: 2 residues within 4Å: Chain C: E.299, N.300 No protein-ligand interaction detected (PLIP) NAG.30: 3 residues within 4Å: Chain C: R.212, M.237, N.239 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.212, C:R.212, C:N.239 NAG.31: 6 residues within 4Å: Chain C: P.413, N.440, P.447, H.449, V.451, Q.453 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.413, C:Q.453 NAG.33: 1 residues within 4Å: Chain D: N.438 No protein-ligand interaction detected (PLIP) NAG.34: 1 residues within 4Å: Chain D: N.70 No protein-ligand interaction detected (PLIP)

2 x GLY: GLYCINE(Non-covalent)

GLY.22: 9 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.516, A:T.518, A:S.688, A:S.688 Salt bridges: A:R.523 GLY.32: 9 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.516, C:T.518, C:S.688, C:S.688 Salt bridges: C:R.523

2 x GLU: GLUTAMIC ACID(Non-covalent)(Covalent)

GLU.25: 10 residues within 4Å: Chain B: H.483, S.509, L.510, T.511, R.516, G.686, S.687, T.688, Y.728, D.729 11 PLIP interactions: 8 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.728 Hydrogen bonds: B:S.509, B:T.511, B:T.511, B:S.687, B:T.688, E.25, E.25, E.25 Salt bridges: B:H.483, B:R.516 GLU.35: 10 residues within 4Å: Chain D: H.483, S.509, L.510, T.511, R.516, G.686, S.687, T.688, Y.728, D.729 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:T.511, D:T.511, D:T.511, D:S.687, D:T.688, E.35, E.35 Salt bridges: D:H.483, D:R.516

1 x IWB: methyl 4-[(2~{R})-3-ethanoyl-1-[2-(2-methyl-1~{H}-indol-3-yl)ethyl]-4-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-2-yl]benzoate(Non-covalent)

IWB.26: 15 residues within 4Å: Chain B: D.161, W.162, S.163, A.164, R.194, D.220, A.221, P.222, V.223, K.463, A.466, K.470, F.471, S.472, Y.473 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.164, B:P.222, B:P.222, B:K.463, B:K.470 Hydrogen bonds: B:S.163, B:A.164, B:R.194, B:D.220

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

Related Entries With Identical Sequence