SMTL ID : 6mmm.1

Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' 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

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: N.273, N.276, S.278 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: P.767, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: K.487, N.494, P.686, N.687 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: M.394, N.471 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: P.767, N.771 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain D: P.686, N.687 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.61, A.62 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.203, T.205, A.206 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.239 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.300 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: G.336, R.337, R.346, F.348, N.350, N.368 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.368, T.370, H.371, I.373 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain A: N.440, D.441, G.445, S.446, P.447, H.449 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: M.394, N.471 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.491 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.75, R.76 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: V.339, N.340 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.380 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: I.442, N.443 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.444 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: N.61, A.62 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.203, T.205 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: M.237, L.238, N.239 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain C: K.275, N.276, E.277, S.278, A.279 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.300 Ligand excluded by PLIP NAG.26: 7 residues within 4Å: Chain C: V.334, T.335, G.336, R.337, N.350, N.368 Ligands: NAG.27 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain C: N.368, T.370, H.371, I.373 Ligands: NAG.26 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain C: N.440, S.446, P.447, R.448, H.449 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: R.489, V.490, N.491 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: H.42, N.75 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain D: S.305, K.309, Q.336, F.337, V.339, N.340 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.380, Q.381 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: I.442, N.443 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: K.441, 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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