SMTL ID : 6mmv.1

Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* Extracellular Domain in the '2-Knuckle-Asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

6 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: 3 residues within 4Å: Chain A: I.26, N.28, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: K.487, P.686, N.687 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain C: I.26, N.28, N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.276, S.278, A.279, V.334 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.278, C:S.278 NAG-NAG.5: 4 residues within 4Å: Chain C: N.368, T.370, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: P.767, N.771 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: N.203, T.205, A.206 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: M.237, N.239 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.276 Ligand excluded by PLIP NAG.10: 8 residues within 4Å: Chain A: V.334, T.335, G.336, F.348, N.350, Y.367, G.369 Ligands: NAG.11 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.368, G.369, T.370 Ligands: NAG.10 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.440, G.445, H.449 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: M.394, N.471 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: R.489, V.490, N.491 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: P.767, N.771 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.75 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.340 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: E.379, N.380 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.443 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: K.441, I.442, N.444 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: N.203, T.205 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: M.237, N.239 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.300 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain C: T.335, G.336, R.337, F.348, N.350 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.440, P.447, H.449 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.471 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: V.490, N.491 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: 2 residues within 4Å: Chain D: N.443, T.446 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: I.442, 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: B
Glutamate receptor ionotropic, NMDA 2A: D

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 2A

Glutamate receptor ionotropic, NMDA 2A