SMTL ID : 8e94.1

PYD-106-bound Human GluN1a-GluN2C NMDA receptor in intact conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

4 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: I.26, N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: Q.337, R.364, H.365, N.368 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.276, V.334 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: P.767, N.771 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-NAG.2: 4 residues within 4Å: Chain A: N.368, T.370, H.371 Chain D: Q.426 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 3 residues within 4Å: Chain B: K.513, P.715, N.716 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain C: N.61, A.62, S.84 No protein-ligand interaction detected (PLIP)

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.8: 2 residues within 4Å: Chain A: T.335, N.350 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.335, A:N.350 NAG.9: 2 residues within 4Å: Chain A: N.276, V.334 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain A: P.767, N.771 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.771 NAG.11: 1 residues within 4Å: Chain A: N.471 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.471 NAG.13: 1 residues within 4Å: Chain C: N.350 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.350 NAG.14: 2 residues within 4Å: Chain C: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain C: N.368, G.369, T.370 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.370 NAG.16: 3 residues within 4Å: Chain D: R.364, H.365, N.368 No protein-ligand interaction detected (PLIP)

1 x IWB: methyl 4-[(2~{R})-3-ethanoyl-1-[2-(2-methyl-1~{H}-indol-3-yl)ethyl]-4-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-2-yl]benzoate(Non-covalent)

IWB.12: 9 residues within 4Å: Chain B: W.193, R.225, L.227, P.253, R.498, K.501, F.502, S.503, Y.504 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.227 Hydrogen bonds: B:R.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chou, T.H. et al., Structural insights into assembly and function of GluN1-2C, GluN1-2A-2C, and GluN1-2D NMDARs. Mol.Cell (2022)

Release Date

2022-12-07

Peptides

Glutamate receptor ionotropic, NMDA 1: AC
Glutamate receptor ionotropic, NMDA 2C: BD

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 2C

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