SMTL ID : 6mmn.1

Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 8.0

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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.1: 5 residues within 4Å: Chain A: N.273, N.276, E.277, S.278, V.334 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.334 NAG-NAG.2: 3 residues within 4Å: Chain A: N.368, T.370, H.371 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.440, Q.453 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: P.767, Q.770, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: S.305, N.340 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: K.484, P.686, N.687 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain C: N.273, N.276, S.278, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: V.334, T.335, N.350 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.368, T.370, H.371 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.440, S.446, R.448, H.449 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain D: P.686, N.687 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: N.61, A.62, T.63 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.203, T.205 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: M.237, L.238, N.239 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.300 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: I.272, V.334, T.335, N.350 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.471 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: V.490, N.491 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: L.73, M.74, N.75, R.76 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.380 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: I.442, N.443 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: I.442, N.443, N.444 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: N.61, A.62, T.63 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.203, T.205, A.206 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: M.237, N.239 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: E.299, N.300 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.471 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: R.489, N.491 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: L.73, M.74, N.75, R.76 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain D: N.340 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: E.379, N.380 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: I.442, N.443 Ligand excluded by PLIP NAG.34: 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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