SMTL ID : 7yfi.1

Structure of the Rat tri-heteromeric GluN1-GluN2A-GluN2C NMDA receptor in complex with glycine and glutamate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

9 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: 6 residues within 4Å: Chain A: I.26, N.28, N.61, A.62, T.63, S.84 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.368, G.369, I.373 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.471 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: M.394, P.767, W.768, N.771 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: K.485, P.687, N.688, R.712 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain C: I.26, N.28, N.61, A.62, T.63, S.84, S.85 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.203, T.205, A.206, M.209 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.205 NAG-NAG.9: 1 residues within 4Å: Chain C: N.471 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain D: R.305, Q.306, R.333, H.334, N.337 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:R.333 Hydrogen bonds: D:R.305, D:Q.306

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.6: 3 residues within 4Å: Chain C: N.276, S.278, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 5 residues within 4Å: Chain D: K.482, V.487, P.684, N.685, R.709 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain A: N.203, T.205 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: R.212, N.239 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.273, N.276, V.334 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: E.299, N.300 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.350, I.366, N.368 Ligands: NAG-NAG.2 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: N.440, D.441, S.446, H.449, V.451 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: V.490, N.491, N.492 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: H.43, N.76 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.341 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.381 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.445 Ligands: NAG.24 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.444, N.445, S.446 Ligands: NAG.23 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: R.212, L.238, N.239 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: E.299, N.300 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain C: N.368, G.369, T.370, H.371, I.373 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain C: T.335, G.336, F.348, N.350, N.368 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: N.440, G.445, H.449, V.451 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.491 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: M.394, P.767, W.768, N.771 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: G.68, N.70 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.438, N.480 Ligand excluded by PLIP

2 x GLY: GLYCINE(Non-covalent)

GLY.19: 9 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.688, W.731, D.732, F.758 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.516, A:T.518, A:T.518, A:S.688 Salt bridges: A:R.523 GLY.33: 10 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.687, S.688, W.731, D.732, F.758 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain C Hydrogen bonds: G.33, C:P.516, C:P.516, C:T.518, C:S.688 Salt bridges: C:R.523

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.25: 10 residues within 4Å: Chain B: H.486, S.512, T.514, R.519, G.689, S.690, T.691, Y.731, D.732, Y.762 14 PLIP interactions: 12 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.731, B:D.732 Hydrogen bonds: B:T.514, B:T.514, B:S.690, B:T.691, B:T.691, B:D.732, B:D.732, B:Y.762, E.25, E.25 Salt bridges: B:H.486, B:R.519 GLU.36: 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 12 PLIP interactions: 11 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.728, D:D.729 Hydrogen bonds: D:S.509, D:T.511, D:T.511, D:S.687, D:T.688, D:Y.759, D:Y.759, E.36 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: B
Glutamate receptor ionotropic, NMDA 2C: D

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.
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Glutamate receptor ionotropic, NMDA 1

Glutamate receptor

Glutamate receptor ionotropic, NMDA 2C