SMTL ID : 6ubs.1

Full length Glycine receptor reconstituted in lipid nanodisc in Apo/Resting conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 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: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain E: P.59, P.60, N.62, I.191 No protein-ligand interaction detected (PLIP)

10 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.6: 2 residues within 4Å: Chain A: I.427, W.430 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.427 Salt bridges: A:K.434 PX4.8: 2 residues within 4Å: Chain B: I.427, W.430 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.427 Salt bridges: B:K.434 PX4.10: 1 residues within 4Å: Chain B: G.245 No protein-ligand interaction detected (PLIP) PX4.11: 1 residues within 4Å: Chain C: G.245 No protein-ligand interaction detected (PLIP) PX4.12: 2 residues within 4Å: Chain C: I.427, W.430 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.427 Salt bridges: C:K.434 PX4.14: 1 residues within 4Å: Chain D: G.245 No protein-ligand interaction detected (PLIP) PX4.15: 2 residues within 4Å: Chain D: I.427, W.430 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.427 Salt bridges: D:K.434 PX4.17: 1 residues within 4Å: Chain E: G.245 No protein-ligand interaction detected (PLIP) PX4.18: 1 residues within 4Å: Chain A: G.245 No protein-ligand interaction detected (PLIP) PX4.19: 2 residues within 4Å: Chain E: I.427, W.430 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.427 Salt bridges: E:K.434

5 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.7: 5 residues within 4Å: Chain A: F.319, S.320, L.323, F.418, V.421 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.319, A:L.323, A:F.418, A:V.421 PIO.9: 5 residues within 4Å: Chain B: F.319, S.320, L.323, F.418, V.421 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.319, B:L.323, B:F.418, B:V.421 PIO.13: 5 residues within 4Å: Chain C: F.319, S.320, L.323, F.418, V.421 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.319, C:L.323, C:F.418, C:V.421 PIO.16: 5 residues within 4Å: Chain D: F.319, S.320, L.323, F.418, V.421 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.319, D:L.323, D:F.418, D:V.421 PIO.20: 5 residues within 4Å: Chain E: F.319, S.320, L.323, F.418, V.421 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.319, E:L.323, E:F.418, E:V.421

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs. Nat Commun (2020)

Release Date

2020-07-29

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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