SMTL ID : 7m6o.1

Full length alpha1 Glycine receptor in presence of 0.1mM Glycine and 32uM Tetrahydrocannabinol

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.84 Å

Oligo State

homo-pentamer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.55, P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55, A:P.60 NAG.5: 4 residues within 4Å: Chain B: N.55, P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.55, B:P.60 NAG.8: 4 residues within 4Å: Chain C: N.55, P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.55, C:P.60 NAG.11: 4 residues within 4Å: Chain D: N.55, P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.55, D:P.60 NAG.14: 4 residues within 4Å: Chain E: N.55, P.59, P.60, N.62 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.55, E:P.60

5 x TCI: (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6H-benzo[c]chromen-1-ol(Non-covalent)

TCI.2: 4 residues within 4Å: Chain A: S.320, A.417, F.418, V.421 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.417, A:F.418, A:F.418 Hydrogen bonds: A:S.320 TCI.6: 4 residues within 4Å: Chain B: S.320, A.417, F.418, V.421 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.417, B:F.418, B:F.418 Hydrogen bonds: B:S.320 TCI.9: 4 residues within 4Å: Chain C: S.320, A.417, F.418, V.421 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.417, C:F.418, C:F.418 Hydrogen bonds: C:S.320 TCI.12: 4 residues within 4Å: Chain D: S.320, A.417, F.418, V.421 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:A.417, D:F.418, D:F.418 Hydrogen bonds: D:S.320 TCI.15: 4 residues within 4Å: Chain E: S.320, A.417, F.418, V.421 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:A.417, E:F.418, E:F.418 Hydrogen bonds: E:S.320

5 x GLY: GLYCINE(Non-covalent)

GLY.3: 7 residues within 4Å: Chain A: F.87, R.89, L.141, S.153 Chain E: F.183, T.228, F.231 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.153, E:F.183, E:T.228, G.3, G.3 Salt bridges: A:R.89 GLY.4: 7 residues within 4Å: Chain A: F.183, T.228, F.231 Chain B: F.87, R.89, L.141, S.153 6 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: G.4, G.4, A:F.183, A:T.228, B:S.153 Salt bridges: B:R.89 GLY.7: 7 residues within 4Å: Chain B: F.183, T.228, F.231 Chain C: F.87, R.89, L.141, S.153 6 PLIP interactions: 2 interactions with chain C, 2 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: C:S.153, G.7, G.7, B:F.183, B:T.228 Salt bridges: C:R.89 GLY.10: 7 residues within 4Å: Chain C: F.183, T.228, F.231 Chain D: F.87, R.89, L.141, S.153 6 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: C:F.183, C:T.228, D:S.153, G.10, G.10 Salt bridges: D:R.89 GLY.13: 7 residues within 4Å: Chain D: F.183, T.228, F.231 Chain E: F.87, R.89, L.141, S.153 6 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: E:S.153, D:F.183, D:T.228, G.13, G.13 Salt bridges: E:R.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Structural basis for cannabinoid-induced potentiation of alpha1-glycine receptors in lipid nanodiscs. Nat Commun (2022)

Release Date

2022-08-03

Peptides

Glycine receptor subunit alphaZ1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Glycine receptor subunit alphaZ1

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