SMTL ID : 7yfr.1

Structure of GluN1a E698C-GluN2D NMDA receptor in cystines non-crosslinked state.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

7 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: 5 residues within 4Å: Chain A: N.61, A.62, S.84, S.85, Q.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.84 NAG-NAG.2: 3 residues within 4Å: Chain A: P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.440, P.447 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: V.713, P.714, N.715, Q.738 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: P.767, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain C: N.61, A.62, T.63, S.84, S.85, Q.86 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.84 NAG-NAG.7: 4 residues within 4Å: Chain D: V.713, P.714, N.715, Q.738 No protein-ligand interaction detected (PLIP)

2 x GLY: GLYCINE(Non-covalent)

GLY.8: 7 residues within 4Å: Chain A: F.484, P.516, L.517, T.518, R.523, S.688, D.732 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain A Hydrogen bonds: G.8, A:T.518, A:T.518, A:T.518, A:S.688, A:S.688 Salt bridges: A:R.523 GLY.12: 7 residues within 4Å: Chain C: F.484, P.516, L.517, T.518, R.523, S.688, D.732 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain C Hydrogen bonds: G.12, C:T.518, C:T.518, C:T.518, C:S.688, C:S.688 Salt bridges: C:R.523

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

NAG.9: 3 residues within 4Å: Chain A: N.203, T.205, M.237 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.205 Hydrogen bonds: A:N.203 NAG.10: 1 residues within 4Å: Chain A: N.471 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.471 NAG.13: 5 residues within 4Å: Chain C: N.440, P.447, R.448, A.480, D.481 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.448 NAG.14: 2 residues within 4Å: Chain C: T.396, N.471 No protein-ligand interaction detected (PLIP) NAG.15: 5 residues within 4Å: Chain C: N.203, T.205, A.234, M.237, L.238 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.234, C:L.238 Hydrogen bonds: C:N.203

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.11: 10 residues within 4Å: Chain B: H.513, L.540, T.541, R.546, G.716, S.717, T.718, Y.758, D.759, Y.789 12 PLIP interactions: 9 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.758 Hydrogen bonds: B:T.541, B:T.541, B:S.717, B:T.718, B:D.759, B:D.759, E.11, E.11, E.11 Salt bridges: B:H.513, B:R.546 GLU.16: 10 residues within 4Å: Chain D: H.513, L.540, T.541, R.546, G.716, S.717, T.718, Y.758, D.759, Y.789 12 PLIP interactions: 9 interactions with chain D, 3 Ligand-Ligand interactions Hydrophobic interactions: D:Y.758 Hydrogen bonds: D:T.541, D:T.541, D:S.717, D:T.718, D:D.759, D:D.759, E.16, E.16, E.16 Salt bridges: D:H.513, D:R.546

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

2023-04-12

Peptides

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

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 ionotropic, NMDA 2D

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