SMTL ID : 6mmx.1

Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* in the 'Extended' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4

Coordinates

PDB Format Compare

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: I.26, N.28, N.61, A.62, T.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.62 NAG-NAG.2: 4 residues within 4Å: Chain A: G.336, R.337, R.346, N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.368, T.370, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.440, S.446, H.449 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: E.379, N.380 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.368, T.370, H.371 No protein-ligand interaction detected (PLIP)

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

NAG.8: 3 residues within 4Å: Chain A: K.202, N.203, T.205 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: M.237, L.238, N.239 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: K.275, N.276, E.277, S.278 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: E.299, N.300 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.471 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.491 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: M.470, P.767, N.771 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: L.73, M.74, N.75 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.340 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.443, T.446 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: I.442, N.444 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain C: I.26, Q.59, N.61 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: M.237, L.238, N.239 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: N.276, E.277, S.278, A.279 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: E.299, N.300 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain C: I.272, T.335, G.336, R.337, F.348, N.350 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.440, H.449 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.471 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.491 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: P.767, N.771 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain D: N.75 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain D: N.340 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: E.379, N.380 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: I.442, N.443, E.448 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain D: N.444 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jalali-Yazdi, F. et al., Mechanisms for Zinc and Proton Inhibition of the GluN1/GluN2A NMDA Receptor. Cell (2018)

Release Date

2018-11-28

Peptides

Glutamate receptor ionotropic, NMDA 1: AC
Glutamate receptor ionotropic, NMDA 2A: 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 2A

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