SMTL ID : 9bwb.1

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in a 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: 7 residues within 4Å: Chain A: F.192, Y.235, T.237, F.240 Chain B: F.96, R.98, S.162 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.162, A:F.192, A:T.237 Salt bridges: B:R.98 GLY.16: 7 residues within 4Å: Chain A: F.96, R.98, S.162 Chain E: F.192, Y.235, T.237, F.240 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:S.162, E:F.192, E:T.237 Salt bridges: A:R.98 GLY.17: 7 residues within 4Å: Chain B: F.192, Y.235, T.237, F.240 Chain C: F.96, R.98, 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: 7 residues within 4Å: Chain C: F.192, Y.235, T.237, F.240 Chain D: F.96, R.98, 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: 7 residues within 4Å: Chain D: F.192, Y.235, T.237, F.240 Chain E: F.96, R.98, S.162 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:S.162, D:F.192, D:T.237 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-functional Binders)(Non-covalent)

PIO.7: 1 residues within 4Å: Ligands: PIO.9 No protein-ligand interaction detected (PLIP) PIO.8: 1 residues within 4Å: Ligands: PIO.50 No protein-ligand interaction detected (PLIP) PIO.9: 2 residues within 4Å: Chain A: W.448 Ligands: PIO.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.452 PIO.10: 2 residues within 4Å: Chain A: W.276 Ligands: PX4.11 No protein-ligand interaction detected (PLIP) PIO.15: 4 residues within 4Å: Chain A: S.311, V.313 Chain B: I.258 Ligands: PIO.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.258, A:V.313 PIO.18: 1 residues within 4Å: Ligands: PIO.20 No protein-ligand interaction detected (PLIP) PIO.19: 1 residues within 4Å: Ligands: PIO.15 No protein-ligand interaction detected (PLIP) PIO.20: 2 residues within 4Å: Chain B: W.448 Ligands: PIO.18 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.452 PIO.21: 2 residues within 4Å: Chain B: W.276 Ligands: PX4.22 No protein-ligand interaction detected (PLIP) PIO.26: 4 residues within 4Å: Chain B: S.311, V.313 Chain C: I.258 Ligands: PIO.29 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.313, C:I.258 PIO.28: 1 residues within 4Å: Ligands: PIO.30 No protein-ligand interaction detected (PLIP) PIO.29: 1 residues within 4Å: Ligands: PIO.26 No protein-ligand interaction detected (PLIP) PIO.30: 2 residues within 4Å: Chain C: W.448 Ligands: PIO.28 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.452 PIO.31: 2 residues within 4Å: Chain C: W.276 Ligands: PX4.32 No protein-ligand interaction detected (PLIP) PIO.36: 4 residues within 4Å: Chain C: S.311, V.313 Chain D: I.258 Ligands: PIO.39 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.258, C:V.313 PIO.38: 1 residues within 4Å: Ligands: PIO.40 No protein-ligand interaction detected (PLIP) PIO.39: 1 residues within 4Å: Ligands: PIO.36 No protein-ligand interaction detected (PLIP) PIO.40: 2 residues within 4Å: Chain D: W.448 Ligands: PIO.38 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.452 PIO.41: 2 residues within 4Å: Chain D: W.276 Ligands: PX4.42 No protein-ligand interaction detected (PLIP) PIO.46: 4 residues within 4Å: Chain D: S.311, V.313 Chain E: I.258 Ligands: PIO.52 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:V.313, E:I.258 PIO.50: 4 residues within 4Å: Chain A: I.258 Chain E: S.311, V.313 Ligands: PIO.8 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:V.313, A:I.258 PIO.51: 1 residues within 4Å: Ligands: PIO.53 No protein-ligand interaction detected (PLIP) PIO.52: 1 residues within 4Å: Ligands: PIO.46 No protein-ligand interaction detected (PLIP) PIO.53: 2 residues within 4Å: Chain E: W.448 Ligands: PIO.51 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:K.452 PIO.54: 2 residues within 4Å: Chain E: W.276 Ligands: PX4.55 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: V.273, W.276 Chain E: F.339 Ligands: PIO.10, PX4.47 Ligand excluded by PLIP PX4.12: 3 residues within 4Å: Chain A: L.325, I.428 Ligands: PX4.22 Ligand excluded by PLIP PX4.13: 2 residues within 4Å: Chain A: I.431, C.435 Ligand excluded by PLIP PX4.14: 4 residues within 4Å: Chain A: I.318, I.442, I.450, Y.451 Ligand excluded by PLIP PX4.22: 5 residues within 4Å: Chain A: F.339 Chain B: V.273, W.276 Ligands: PX4.12, PIO.21 Ligand excluded by PLIP PX4.23: 3 residues within 4Å: Chain B: L.325, I.428 Ligands: PX4.32 Ligand excluded by PLIP PX4.24: 2 residues within 4Å: Chain B: I.431, C.435 Ligand excluded by PLIP PX4.25: 4 residues within 4Å: Chain B: I.318, I.442, I.450, Y.451 Ligand excluded by PLIP PX4.32: 5 residues within 4Å: Chain B: F.339 Chain C: V.273, W.276 Ligands: PX4.23, PIO.31 Ligand excluded by PLIP PX4.33: 3 residues within 4Å: Chain C: L.325, I.428 Ligands: PX4.42 Ligand excluded by PLIP PX4.34: 2 residues within 4Å: Chain C: I.431, C.435 Ligand excluded by PLIP PX4.35: 4 residues within 4Å: Chain C: I.318, I.442, I.450, Y.451 Ligand excluded by PLIP PX4.42: 5 residues within 4Å: Chain C: F.339 Chain D: V.273, W.276 Ligands: PX4.33, PIO.41 Ligand excluded by PLIP PX4.43: 3 residues within 4Å: Chain D: L.325, I.428 Ligands: PX4.55 Ligand excluded by PLIP PX4.44: 2 residues within 4Å: Chain D: I.431, C.435 Ligand excluded by PLIP PX4.45: 4 residues within 4Å: Chain D: I.318, I.442, I.450, Y.451 Ligand excluded by PLIP PX4.47: 3 residues within 4Å: Chain E: L.325, I.428 Ligands: PX4.11 Ligand excluded by PLIP PX4.48: 2 residues within 4Å: Chain E: I.431, C.435 Ligand excluded by PLIP PX4.49: 4 residues within 4Å: Chain E: I.318, I.442, I.450, Y.451 Ligand excluded by PLIP PX4.55: 5 residues within 4Å: Chain D: F.339 Chain E: V.273, W.276 Ligands: PX4.43, PIO.54 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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