SMTL ID : 9bwe.1

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine at pH 6.4 in an intermediate 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)

30 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: 3 residues within 4Å: Chain A: W.448, K.452 Ligands: PIO.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.448 PIO.7: 6 residues within 4Å: Chain A: M.253, L.265, N.444, W.448, K.452 Ligands: PIO.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.265 Salt bridges: A:K.452 PIO.8: 3 residues within 4Å: Chain A: L.257, I.258 Chain E: S.311 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.311 Hydrophobic interactions: A:L.257, A:I.258 PIO.9: 1 residues within 4Å: Chain A: I.262 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.262 PIO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PIO.11: 3 residues within 4Å: Chain A: F.339, V.340 Chain B: W.276 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.340, B:W.276 PIO.12: 3 residues within 4Å: Chain A: S.311 Chain B: L.257, I.258 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.257, B:I.258 Hydrogen bonds: A:S.311 PIO.16: 3 residues within 4Å: Chain B: W.448, K.452 Ligands: PIO.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.448 PIO.17: 6 residues within 4Å: Chain B: M.253, L.265, N.444, W.448, K.452 Ligands: PIO.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.265 Salt bridges: B:K.452 PIO.18: 1 residues within 4Å: Chain B: I.262 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.262 PIO.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PIO.20: 3 residues within 4Å: Chain B: A.336, F.339 Chain C: W.276 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.276, B:F.339 PIO.21: 3 residues within 4Å: Chain B: S.311 Chain C: L.257, I.258 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.257, C:I.258 Hydrogen bonds: B:S.311 PIO.25: 3 residues within 4Å: Chain C: W.448, K.452 Ligands: PIO.26 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.448 PIO.26: 6 residues within 4Å: Chain C: M.253, L.265, N.444, W.448, K.452 Ligands: PIO.25 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.265 Salt bridges: C:K.452 PIO.27: 1 residues within 4Å: Chain C: I.262 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.262 PIO.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PIO.29: 4 residues within 4Å: Chain C: A.336, F.339, V.340 Chain D: W.276 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.339, C:V.340, D:W.276 PIO.31: 3 residues within 4Å: Chain D: W.448, K.452 Ligands: PIO.32 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.448 PIO.32: 6 residues within 4Å: Chain D: M.253, L.265, N.444, W.448, K.452 Ligands: PIO.31 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.265 Salt bridges: D:K.452 PIO.33: 3 residues within 4Å: Chain C: S.311 Chain D: L.257, I.258 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.257, D:I.258 Hydrogen bonds: C:S.311 PIO.34: 1 residues within 4Å: Chain D: I.262 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.262 PIO.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PIO.36: 3 residues within 4Å: Chain D: A.336, F.339 Chain E: W.276 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:F.339, E:W.276 PIO.37: 3 residues within 4Å: Chain D: S.311 Chain E: L.257, I.258 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:L.257, E:I.258 Hydrogen bonds: D:S.311 PIO.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PIO.40: 4 residues within 4Å: Chain A: W.276 Chain E: A.336, F.339, V.340 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:W.276, E:F.339, E:V.340 PIO.43: 3 residues within 4Å: Chain E: W.448, K.452 Ligands: PIO.44 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.448 PIO.44: 6 residues within 4Å: Chain E: M.253, L.265, N.444, W.448, K.452 Ligands: PIO.43 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.265 Salt bridges: E:K.452 PIO.45: 1 residues within 4Å: Chain E: I.262 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.262

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

PX4.13: 5 residues within 4Å: Chain A: F.326, S.329, I.431, C.435, F.436 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.326, A:F.436 PX4.22: 5 residues within 4Å: Chain B: F.326, S.329, I.428, I.431, F.436 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.326, B:I.428, B:F.436 PX4.30: 6 residues within 4Å: Chain C: F.326, S.329, I.428, I.431, C.435, F.436 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.326, C:I.428, C:F.436 PX4.38: 5 residues within 4Å: Chain D: F.326, S.329, I.428, I.431, F.436 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.326, D:I.428, D:F.436 PX4.41: 5 residues within 4Å: Chain E: F.326, S.329, I.431, C.435, F.436 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.326, E:F.436

5 x GLY: GLYCINE(Non-covalent)

GLY.14: 7 residues within 4Å: Chain A: R.98, L.150, S.162 Chain E: F.192, Y.235, T.237, F.240 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.191, E:T.237, A:S.162 Salt bridges: A:R.98 GLY.15: 7 residues within 4Å: Chain A: F.192, Y.235, T.237, F.240 Chain B: R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.191, A:T.237, B:S.162 Salt bridges: B:R.98 GLY.23: 7 residues within 4Å: Chain B: F.192, Y.235, T.237, F.240 Chain C: 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:S.191, B:T.237 Salt bridges: C:R.98 GLY.24: 7 residues within 4Å: Chain C: F.192, Y.235, T.237, F.240 Chain D: R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.191, C:T.237, D:S.162 Salt bridges: D:R.98 GLY.42: 7 residues within 4Å: Chain D: F.192, Y.235, T.237, F.240 Chain E: R.98, L.150, S.162 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.191, D:T.237, E:S.162 Salt bridges: E:R.98

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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