SMTL ID : 7yfg.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

NAG-NAG.1: 1 residues within 4Å: Chain A: N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: T.335, G.336, R.337, F.348, A.349, N.350 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.337 NAG-NAG.3: 3 residues within 4Å: Chain A: P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: Q.306, H.334, N.337 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.306 NAG-NAG.6: 3 residues within 4Å: Chain A: I.26, N.61, A.62 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.239 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.471 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: I.26, N.28, N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: M.237, N.239 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.276, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: M.394, P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.471 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.368, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain D: Q.306, H.334, N.337 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.306

1 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.5: 4 residues within 4Å: Chain A: N.368, T.370, I.373 Chain D: Q.395 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.395

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

NAG.18: 1 residues within 4Å: Chain A: N.300 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain A: N.491, N.492 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.491, A:N.492 NAG.20: 6 residues within 4Å: Chain A: P.413, T.414, N.440, T.442, V.451, P.452 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.413, A:T.414 Hydrogen bonds: A:T.442 NAG.22: 4 residues within 4Å: Chain B: K.485, V.487, N.685, R.709 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.709 Hydrogen bonds: B:K.485, B:N.685, B:N.685 NAG.23: 1 residues within 4Å: Chain B: N.70 No protein-ligand interaction detected (PLIP) NAG.24: 6 residues within 4Å: Chain B: N.438, F.441, S.442, L.446, P.448, Y.449 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.442 NAG.26: 1 residues within 4Å: Chain C: N.300 No protein-ligand interaction detected (PLIP) NAG.27: 4 residues within 4Å: Chain C: T.335, G.336, N.350, I.366 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.350 NAG.28: 2 residues within 4Å: Chain C: V.490, N.491 No protein-ligand interaction detected (PLIP) NAG.29: 2 residues within 4Å: Chain C: N.440, P.447 No protein-ligand interaction detected (PLIP) NAG.31: 2 residues within 4Å: Chain D: K.482, N.685 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.482 NAG.32: 1 residues within 4Å: Chain D: N.70 No protein-ligand interaction detected (PLIP) NAG.33: 2 residues within 4Å: Chain D: N.438, H.439 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.438, D:H.439

2 x GLY: GLYCINE(Non-covalent)

GLY.21: 10 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732, F.758 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.516, A:T.518, A:S.688 Salt bridges: A:R.523 GLY.30: 8 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.687, S.688, D.732 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:P.516, C:T.518, C:S.688, C:S.688, C:D.732 Salt bridges: C:R.523

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.25: 11 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, Y.759 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.728 Hydrogen bonds: B:T.511, B:T.511, B:S.687, B:T.688, B:D.729, B:Y.759, E.25, E.25 Salt bridges: B:H.483, B:R.516 GLU.34: 11 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, Y.759 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain D Hydrogen bonds: E.34, D:S.509, D:T.511, D:S.687, D:T.688, D:D.729 Hydrophobic interactions: D:Y.728 Salt bridges: D:H.483, D:R.516

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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