SMTL ID : 9c7r.1

Diheteromeric GluN1/GluN2A (M817V) in digitonin complexed with glycine, glutamate, and GNE-4123

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

20 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: 4 residues within 4Å: Chain A: N.28, N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.276, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: T.335, G.336, R.337, F.348, N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.368, G.369, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.340 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.380 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: K.484, P.686, N.687, R.711 Ligands: NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: I.26, N.28, N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.239 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.276, A.279, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: G.333, G.336, N.350, I.366, N.368 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.368, H.371, I.373 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.471 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: P.767, W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain D: N.340 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain D: N.380 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain D: P.686, N.687, R.711 Ligands: NAG.34 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain A: R.212, N.239 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.300 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.440, D.441, V.451 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.471 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.75 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.443 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.444 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.541 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: E.299, N.300 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.440, D.441, V.451 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.491, N.492 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain D: N.75 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.443, S.445 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.444 Ligands: NAG-NAG.20 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain D: N.541 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jalali-Yazdi, F. et al., Diheteromeric GluN1/GluN2A (M817V), in complex with glycine, glutamate, and GNE-4123. To Be Published

Release Date

2025-09-24

Peptides

Glutamate receptor ionotropic, NMDA 1, Green fluorescent protein chimera: AC
Glutamate receptor ionotropic, NMDA 2A, Green fluorescent protein chimera: 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, Green fluorescent protein chimera

Glutamate receptor ionotropic, NMDA 2A, Green fluorescent protein chimera

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