SMTL ID : 9bvj.1

Homomeric alpha3 glycine receptor in the presence of 1 mM glycine in an desensitized 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)

5 x GLY: GLYCINE(Non-covalent)

GLY.6: 9 residues within 4Å: Chain A: S.191, F.192, Y.235, T.237, F.240 Chain B: F.96, R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.192, A:T.237, B:S.162 Salt bridges: B:R.98 GLY.16: 9 residues within 4Å: Chain A: F.96, R.98, L.150, S.162 Chain E: S.191, F.192, Y.235, T.237, F.240 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:F.192, E:T.237, A:S.162 Salt bridges: A:R.98 GLY.17: 9 residues within 4Å: Chain B: S.191, F.192, Y.235, T.237, F.240 Chain C: F.96, R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.162, B:F.192, B:T.237 Salt bridges: C:R.98 GLY.27: 9 residues within 4Å: Chain C: S.191, F.192, Y.235, T.237, F.240 Chain D: F.96, R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.162, C:F.192, C:T.237 Salt bridges: D:R.98 GLY.37: 9 residues within 4Å: Chain D: S.191, F.192, Y.235, T.237, F.240 Chain E: F.96, R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:F.192, D:T.237, E:S.162 Salt bridges: E:R.98

25 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: 2 residues within 4Å: Chain A: W.448 Ligands: PIO.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.448 PIO.8: 3 residues within 4Å: Chain A: L.265 Ligands: PIO.9, PIO.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.265 PIO.9: 4 residues within 4Å: Chain A: L.257, W.448 Ligands: PIO.7, PIO.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.257 Salt bridges: A:K.452 PIO.10: 1 residues within 4Å: Chain A: W.276 No protein-ligand interaction detected (PLIP) PIO.12: 5 residues within 4Å: Chain A: S.311, V.313 Chain B: I.258, I.262 Ligands: PIO.19 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.258, B:I.262, A:V.313 PIO.18: 2 residues within 4Å: Chain B: W.448 Ligands: PIO.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.448 PIO.19: 3 residues within 4Å: Chain B: L.265 Ligands: PIO.12, PIO.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.265 PIO.20: 4 residues within 4Å: Chain B: L.257, W.448 Ligands: PIO.18, PIO.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.257 Salt bridges: B:K.452 PIO.21: 1 residues within 4Å: Chain B: W.276 No protein-ligand interaction detected (PLIP) PIO.23: 5 residues within 4Å: Chain B: S.311, V.313 Chain C: I.258, I.262 Ligands: PIO.29 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.258, C:I.262, B:V.313 PIO.28: 2 residues within 4Å: Chain C: W.448 Ligands: PIO.30 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.448 PIO.29: 3 residues within 4Å: Chain C: L.265 Ligands: PIO.23, PIO.30 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.265 PIO.30: 4 residues within 4Å: Chain C: L.257, W.448 Ligands: PIO.28, PIO.29 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.257 Salt bridges: C:K.452 PIO.31: 1 residues within 4Å: Chain C: W.276 No protein-ligand interaction detected (PLIP) PIO.33: 5 residues within 4Å: Chain C: S.311, V.313 Chain D: I.258, I.262 Ligands: PIO.39 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.313, D:I.258, D:I.262 PIO.38: 2 residues within 4Å: Chain D: W.448 Ligands: PIO.40 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.448 PIO.39: 3 residues within 4Å: Chain D: L.265 Ligands: PIO.33, PIO.40 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.265 PIO.40: 4 residues within 4Å: Chain D: L.257, W.448 Ligands: PIO.38, PIO.39 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.257 Salt bridges: D:K.452 PIO.41: 1 residues within 4Å: Chain D: W.276 No protein-ligand interaction detected (PLIP) PIO.43: 5 residues within 4Å: Chain D: S.311, V.313 Chain E: I.258, I.262 Ligands: PIO.52 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.258, E:I.262, D:V.313 PIO.47: 5 residues within 4Å: Chain A: I.258, I.262 Chain E: S.311, V.313 Ligands: PIO.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.258, A:I.262, E:V.313 PIO.51: 2 residues within 4Å: Chain E: W.448 Ligands: PIO.53 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.448 PIO.52: 3 residues within 4Å: Chain E: L.265 Ligands: PIO.43, PIO.53 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.265 PIO.53: 4 residues within 4Å: Chain E: L.257, W.448 Ligands: PIO.51, PIO.52 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.257 Salt bridges: E:K.452 PIO.54: 1 residues within 4Å: Chain E: W.276 No protein-ligand interaction detected (PLIP)

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

PX4.11: 5 residues within 4Å: Chain A: I.269, W.276 Chain E: L.332, F.339 Ligands: PX4.50 Ligand excluded by PLIP PX4.13: 5 residues within 4Å: Chain A: I.318, I.442, F.443, I.450, Y.451 Ligand excluded by PLIP PX4.14: 6 residues within 4Å: Chain A: L.325, F.326, I.431, C.435, F.436 Ligands: PX4.15 Ligand excluded by PLIP PX4.15: 3 residues within 4Å: Chain A: S.329 Ligands: PX4.14, PX4.22 Ligand excluded by PLIP PX4.22: 5 residues within 4Å: Chain A: L.332, F.339 Chain B: I.269, W.276 Ligands: PX4.15 Ligand excluded by PLIP PX4.24: 5 residues within 4Å: Chain B: I.318, I.442, F.443, I.450, Y.451 Ligand excluded by PLIP PX4.25: 5 residues within 4Å: Chain B: L.325, F.326, C.435, F.436 Ligands: PX4.26 Ligand excluded by PLIP PX4.26: 3 residues within 4Å: Chain B: S.329 Ligands: PX4.25, PX4.32 Ligand excluded by PLIP PX4.32: 5 residues within 4Å: Chain B: L.332, F.339 Chain C: I.269, W.276 Ligands: PX4.26 Ligand excluded by PLIP PX4.34: 5 residues within 4Å: Chain C: I.318, I.442, F.443, I.450, Y.451 Ligand excluded by PLIP PX4.35: 6 residues within 4Å: Chain C: L.325, F.326, I.431, C.435, F.436 Ligands: PX4.36 Ligand excluded by PLIP PX4.36: 3 residues within 4Å: Chain C: S.329 Ligands: PX4.35, PX4.42 Ligand excluded by PLIP PX4.42: 5 residues within 4Å: Chain C: L.332, F.339 Chain D: I.269, W.276 Ligands: PX4.36 Ligand excluded by PLIP PX4.44: 5 residues within 4Å: Chain D: I.318, I.442, F.443, I.450, Y.451 Ligand excluded by PLIP PX4.45: 5 residues within 4Å: Chain D: L.325, F.326, C.435, F.436 Ligands: PX4.46 Ligand excluded by PLIP PX4.46: 3 residues within 4Å: Chain D: S.329 Ligands: PX4.45, PX4.55 Ligand excluded by PLIP PX4.48: 5 residues within 4Å: Chain E: I.318, I.442, F.443, I.450, Y.451 Ligand excluded by PLIP PX4.49: 6 residues within 4Å: Chain E: L.325, F.326, I.431, C.435, F.436 Ligands: PX4.50 Ligand excluded by PLIP PX4.50: 3 residues within 4Å: Chain E: S.329 Ligands: PX4.11, PX4.49 Ligand excluded by PLIP PX4.55: 5 residues within 4Å: Chain D: L.332, F.339 Chain E: I.269, W.276 Ligands: PX4.46 Ligand excluded by PLIP

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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