SMTL ID : 9bwc.1

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in an apo state

Coordinates

PDB Format Compare

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: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain D: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain E: N.64, P.68, P.69, N.71 No protein-ligand interaction detected (PLIP)

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

PX4.6: 5 residues within 4Å: Chain A: G.254, L.257, I.258 Chain E: V.313, V.322 Ligand excluded by PLIP PX4.8: 4 residues within 4Å: Chain A: F.446, I.450, Y.451, R.455 Ligand excluded by PLIP PX4.9: 2 residues within 4Å: Chain A: S.329 Ligands: PX4.10 Ligand excluded by PLIP PX4.10: 5 residues within 4Å: Chain A: F.326, S.329, I.431, F.436 Ligands: PX4.9 Ligand excluded by PLIP PX4.11: 1 residues within 4Å: Chain A: F.339 Ligand excluded by PLIP PX4.14: 5 residues within 4Å: Chain A: V.313, V.322 Chain B: G.254, L.257, I.258 Ligand excluded by PLIP PX4.16: 4 residues within 4Å: Chain B: F.446, I.450, Y.451, R.455 Ligand excluded by PLIP PX4.17: 2 residues within 4Å: Chain B: S.329 Ligands: PX4.18 Ligand excluded by PLIP PX4.18: 5 residues within 4Å: Chain B: F.326, S.329, I.431, F.436 Ligands: PX4.17 Ligand excluded by PLIP PX4.19: 1 residues within 4Å: Chain B: F.339 Ligand excluded by PLIP PX4.21: 5 residues within 4Å: Chain B: V.313, V.322 Chain C: G.254, L.257, I.258 Ligand excluded by PLIP PX4.23: 4 residues within 4Å: Chain C: F.446, I.450, Y.451, R.455 Ligand excluded by PLIP PX4.24: 2 residues within 4Å: Chain C: S.329 Ligands: PX4.25 Ligand excluded by PLIP PX4.25: 5 residues within 4Å: Chain C: F.326, S.329, I.431, F.436 Ligands: PX4.24 Ligand excluded by PLIP PX4.26: 1 residues within 4Å: Chain C: F.339 Ligand excluded by PLIP PX4.28: 5 residues within 4Å: Chain C: V.313, V.322 Chain D: G.254, L.257, I.258 Ligand excluded by PLIP PX4.30: 4 residues within 4Å: Chain D: F.446, I.450, Y.451, R.455 Ligand excluded by PLIP PX4.31: 2 residues within 4Å: Chain D: S.329 Ligands: PX4.32 Ligand excluded by PLIP PX4.32: 5 residues within 4Å: Chain D: F.326, S.329, I.431, F.436 Ligands: PX4.31 Ligand excluded by PLIP PX4.33: 1 residues within 4Å: Chain D: F.339 Ligand excluded by PLIP PX4.34: 4 residues within 4Å: Chain E: F.446, I.450, Y.451, R.455 Ligand excluded by PLIP PX4.35: 2 residues within 4Å: Chain E: S.329 Ligands: PX4.36 Ligand excluded by PLIP PX4.36: 5 residues within 4Å: Chain E: F.326, S.329, I.431, F.436 Ligands: PX4.35 Ligand excluded by PLIP PX4.37: 1 residues within 4Å: Chain E: F.339 Ligand excluded by PLIP PX4.39: 5 residues within 4Å: Chain D: V.313, V.322 Chain E: G.254, L.257, I.258 Ligand excluded by PLIP

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: 3 residues within 4Å: Chain A: L.441, W.448, I.453 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.441, A:W.448 PIO.15: 3 residues within 4Å: Chain B: L.441, W.448, I.453 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.441, B:W.448 PIO.22: 3 residues within 4Å: Chain C: L.441, W.448, I.453 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.441, C:W.448 PIO.29: 3 residues within 4Å: Chain D: L.441, W.448, I.453 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.441, D:W.448 PIO.40: 3 residues within 4Å: Chain E: L.441, W.448, I.453 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.441, E:W.448

5 x GLY: GLYCINE(Non-covalent)

GLY.12: 3 residues within 4Å: Chain A: S.162 Chain E: F.192, Y.235 4 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: G.12, G.12, A:S.162, E:F.192 GLY.13: 3 residues within 4Å: Chain A: F.192, Y.235 Chain B: S.162 4 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: G.13, G.13, B:S.162, A:F.192 GLY.20: 3 residues within 4Å: Chain B: F.192, Y.235 Chain C: S.162 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: B:F.192, C:S.162, G.20, G.20 GLY.27: 3 residues within 4Å: Chain C: F.192, Y.235 Chain D: S.162 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: C:F.192, D:S.162, G.27, G.27 GLY.38: 3 residues within 4Å: Chain D: F.192, Y.235 Chain E: S.162 4 PLIP interactions: 1 interactions with chain D, 2 Ligand-Ligand interactions, 1 interactions with chain E Hydrogen bonds: D:F.192, G.38, G.38, E:S.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kindig, K. et al., Physiological modulation of alpha3 glycine receptors. To Be Published

Release Date

2024-11-13

Peptides

Glycine receptor subunit alpha-3: 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 alpha-3

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