SMTL ID : 9bvh.1

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine 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)

20 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)(Non-functional Binders)

PIO.6: 1 residues within 4Å: Chain A: W.276 No protein-ligand interaction detected (PLIP) PIO.7: 1 residues within 4Å: Ligands: CLR.43 No protein-ligand interaction detected (PLIP) PIO.8: 1 residues within 4Å: Chain A: W.448 No protein-ligand interaction detected (PLIP) PIO.13: 3 residues within 4Å: Chain A: F.446, I.450 Ligands: CLR.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.446, A:I.450 Hydrogen bonds: A:Y.451 PIO.17: 1 residues within 4Å: Chain B: W.276 No protein-ligand interaction detected (PLIP) PIO.18: 1 residues within 4Å: Ligands: CLR.14 No protein-ligand interaction detected (PLIP) PIO.19: 1 residues within 4Å: Chain B: W.448 No protein-ligand interaction detected (PLIP) PIO.22: 3 residues within 4Å: Chain B: F.446, I.450 Ligands: CLR.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.446, B:I.450 Hydrogen bonds: B:Y.451 PIO.26: 1 residues within 4Å: Chain C: W.276 No protein-ligand interaction detected (PLIP) PIO.27: 1 residues within 4Å: Ligands: CLR.23 No protein-ligand interaction detected (PLIP) PIO.28: 1 residues within 4Å: Chain C: W.448 No protein-ligand interaction detected (PLIP) PIO.31: 3 residues within 4Å: Chain C: F.446, I.450 Ligands: CLR.32 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.446, C:I.450 Hydrogen bonds: C:Y.451 PIO.35: 1 residues within 4Å: Chain D: W.276 No protein-ligand interaction detected (PLIP) PIO.36: 1 residues within 4Å: Ligands: CLR.32 No protein-ligand interaction detected (PLIP) PIO.37: 1 residues within 4Å: Chain D: W.448 No protein-ligand interaction detected (PLIP) PIO.40: 3 residues within 4Å: Chain D: F.446, I.450 Ligands: CLR.41 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.446, D:I.450 Hydrogen bonds: D:Y.451 PIO.42: 3 residues within 4Å: Chain E: F.446, I.450 Ligands: CLR.43 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.446, E:I.450 Hydrogen bonds: E:Y.451 PIO.48: 1 residues within 4Å: Chain E: W.276 No protein-ligand interaction detected (PLIP) PIO.49: 1 residues within 4Å: Ligands: CLR.41 No protein-ligand interaction detected (PLIP) PIO.50: 1 residues within 4Å: Chain E: W.448 No protein-ligand interaction detected (PLIP)

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

PX4.9: 2 residues within 4Å: Chain A: N.444, K.452 Ligand excluded by PLIP PX4.10: 3 residues within 4Å: Chain A: W.276 Chain E: L.332, F.339 Ligand excluded by PLIP PX4.11: 5 residues within 4Å: Chain A: F.326, S.432, C.435, F.436 Ligands: PX4.12 Ligand excluded by PLIP PX4.12: 3 residues within 4Å: Chain A: S.329, I.428 Ligands: PX4.11 Ligand excluded by PLIP PX4.15: 2 residues within 4Å: Chain B: N.444, K.452 Ligand excluded by PLIP PX4.16: 3 residues within 4Å: Chain A: L.332, F.339 Chain B: W.276 Ligand excluded by PLIP PX4.20: 5 residues within 4Å: Chain B: F.326, S.432, C.435, F.436 Ligands: PX4.21 Ligand excluded by PLIP PX4.21: 3 residues within 4Å: Chain B: S.329, I.428 Ligands: PX4.20 Ligand excluded by PLIP PX4.24: 2 residues within 4Å: Chain C: N.444, K.452 Ligand excluded by PLIP PX4.25: 2 residues within 4Å: Chain B: F.339 Chain C: W.276 Ligand excluded by PLIP PX4.29: 5 residues within 4Å: Chain C: F.326, S.432, C.435, F.436 Ligands: PX4.30 Ligand excluded by PLIP PX4.30: 3 residues within 4Å: Chain C: S.329, I.428 Ligands: PX4.29 Ligand excluded by PLIP PX4.33: 2 residues within 4Å: Chain D: N.444, K.452 Ligand excluded by PLIP PX4.34: 3 residues within 4Å: Chain C: L.332, F.339 Chain D: W.276 Ligand excluded by PLIP PX4.38: 5 residues within 4Å: Chain D: F.326, S.432, C.435, F.436 Ligands: PX4.39 Ligand excluded by PLIP PX4.39: 3 residues within 4Å: Chain D: S.329, I.428 Ligands: PX4.38 Ligand excluded by PLIP PX4.44: 5 residues within 4Å: Chain E: F.326, S.432, C.435, F.436 Ligands: PX4.45 Ligand excluded by PLIP PX4.45: 3 residues within 4Å: Chain E: S.329, I.428 Ligands: PX4.44 Ligand excluded by PLIP PX4.46: 2 residues within 4Å: Chain E: N.444, K.452 Ligand excluded by PLIP PX4.47: 3 residues within 4Å: Chain D: L.332, F.339 Chain E: W.276 Ligand excluded by PLIP

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.14: 4 residues within 4Å: Chain A: V.313, I.318 Ligands: PIO.13, PIO.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.313, A:I.318 CLR.23: 4 residues within 4Å: Chain B: V.313, I.318 Ligands: PIO.22, PIO.27 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.313, B:I.318 CLR.32: 4 residues within 4Å: Chain C: V.313, I.318 Ligands: PIO.31, PIO.36 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.313, C:I.318 CLR.41: 4 residues within 4Å: Chain D: V.313, I.318 Ligands: PIO.40, PIO.49 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.313, D:I.318 CLR.43: 4 residues within 4Å: Chain E: V.313, I.318 Ligands: PIO.7, PIO.42 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.313, E:I.318

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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