SMTL ID : 6mmi.1

Diheteromeric NMDA receptor GluN1/GluN2A in the 'Splayed-Open' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar zinc chloride, and at pH 7.4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

13 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: 2 residues within 4Å: Chain A: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.276, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: E.299, N.300 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: T.469, M.470, N.471 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.491 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: M.470, W.768, N.771 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: K.484, V.489, P.686, N.687 Ligands: NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: I.26, N.28, N.61, A.62 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.239 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.276, S.278, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.300 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain D: K.484, V.489, P.686, N.687 Ligands: NAG.34 No protein-ligand interaction detected (PLIP)

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

NAG.14: 4 residues within 4Å: Chain A: I.26, N.28, Q.59, N.61 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.239 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: R.337, F.348, N.350, G.369 Ligands: NAG.17 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.368, I.373 Ligands: NAG.16 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.440, S.446, H.449 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: H.42, N.75 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.340 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.380, Q.381 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: I.442, N.443 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: K.441, N.444, T.481 Ligands: NAG-NAG.7 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: T.201, K.202, N.203 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: G.336, R.337, F.348, N.350 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: F.348, N.368, T.370, H.371 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.440, S.446, H.449 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: M.394, N.471 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.491 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: L.73, N.75 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: V.339, N.340 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: E.379, N.380 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain D: I.442, N.443, N.444 Ligands: NAG.34 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: N.444 Ligands: NAG-NAG.13, NAG.33 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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