SMTL ID : 9bu3.1

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine 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: 6 residues within 4Å: Chain A: F.192, T.237, F.240 Chain B: R.98, L.150, 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.7: 6 residues within 4Å: Chain A: R.98, L.150, S.162 Chain E: F.192, 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: 6 residues within 4Å: Chain B: F.192, 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:F.192, B:T.237 Salt bridges: C:R.98 GLY.27: 6 residues within 4Å: Chain C: F.192, 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:F.192, C:T.237, D:S.162 Salt bridges: D:R.98 GLY.37: 7 residues within 4Å: Chain D: F.192, T.237, F.240 Chain E: F.96, R.98, L.150, 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-covalent)(Non-functional Binders)

PIO.8: 2 residues within 4Å: Chain A: I.445 Ligands: PIO.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.445 PIO.9: 2 residues within 4Å: Ligands: PIO.10, PIO.47 No protein-ligand interaction detected (PLIP) PIO.10: 3 residues within 4Å: Chain A: W.448 Ligands: PIO.8, PIO.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.448 Salt bridges: A:K.452 PIO.11: 2 residues within 4Å: Chain A: W.276 Ligands: PX4.12 No protein-ligand interaction detected (PLIP) PIO.13: 3 residues within 4Å: Chain A: S.311 Chain B: I.258 Ligands: PIO.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.258 PIO.18: 2 residues within 4Å: Chain B: I.445 Ligands: PIO.20 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.445 PIO.19: 2 residues within 4Å: Ligands: PIO.13, PIO.20 No protein-ligand interaction detected (PLIP) PIO.20: 3 residues within 4Å: Chain B: W.448 Ligands: PIO.18, PIO.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.448 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.23: 3 residues within 4Å: Chain B: S.311 Chain C: I.258 Ligands: PIO.29 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.258 PIO.28: 2 residues within 4Å: Chain C: I.445 Ligands: PIO.30 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.445 PIO.29: 2 residues within 4Å: Ligands: PIO.23, PIO.30 No protein-ligand interaction detected (PLIP) PIO.30: 3 residues within 4Å: Chain C: W.448 Ligands: PIO.28, PIO.29 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.448 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.33: 3 residues within 4Å: Chain C: S.311 Chain D: I.258 Ligands: PIO.39 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.258 PIO.38: 2 residues within 4Å: Chain D: I.445 Ligands: PIO.40 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.445 PIO.39: 2 residues within 4Å: Ligands: PIO.33, PIO.40 No protein-ligand interaction detected (PLIP) PIO.40: 3 residues within 4Å: Chain D: W.448 Ligands: PIO.38, PIO.39 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.448 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.43: 3 residues within 4Å: Chain D: S.311 Chain E: I.258 Ligands: PIO.52 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.258 PIO.47: 3 residues within 4Å: Chain A: I.258 Chain E: S.311 Ligands: PIO.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.258 PIO.51: 2 residues within 4Å: Chain E: I.445 Ligands: PIO.53 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.445 PIO.52: 2 residues within 4Å: Ligands: PIO.43, PIO.53 No protein-ligand interaction detected (PLIP) PIO.53: 3 residues within 4Å: Chain E: W.448 Ligands: PIO.51, PIO.52 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.448 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)

PX4.12: 8 residues within 4Å: Chain A: V.273, W.276 Chain E: L.332, F.339, V.340, R.424 Ligands: PIO.11, PX4.49 Ligand excluded by PLIP PX4.14: 4 residues within 4Å: Chain A: F.446, I.450, Y.451, L.454 Ligand excluded by PLIP PX4.15: 4 residues within 4Å: Chain A: S.329, A.336 Ligands: PX4.16, PX4.22 Ligand excluded by PLIP PX4.16: 5 residues within 4Å: Chain A: L.325, F.326, I.431, C.435 Ligands: PX4.15 Ligand excluded by PLIP PX4.22: 7 residues within 4Å: Chain A: F.339, V.340, R.424 Chain B: V.273, W.276 Ligands: PX4.15, PIO.21 Ligand excluded by PLIP PX4.24: 5 residues within 4Å: Chain B: F.443, F.446, I.450, Y.451, L.454 Ligand excluded by PLIP PX4.25: 4 residues within 4Å: Chain B: S.329, A.336 Ligands: PX4.26, PX4.32 Ligand excluded by PLIP PX4.26: 5 residues within 4Å: Chain B: L.325, F.326, I.431, C.435 Ligands: PX4.25 Ligand excluded by PLIP PX4.32: 7 residues within 4Å: Chain B: F.339, V.340, R.424 Chain C: V.273, W.276 Ligands: PX4.25, PIO.31 Ligand excluded by PLIP PX4.34: 4 residues within 4Å: Chain C: F.446, I.450, Y.451, L.454 Ligand excluded by PLIP PX4.35: 4 residues within 4Å: Chain C: S.329, A.336 Ligands: PX4.36, PX4.42 Ligand excluded by PLIP PX4.36: 5 residues within 4Å: Chain C: L.325, F.326, I.431, C.435 Ligands: PX4.35 Ligand excluded by PLIP PX4.42: 7 residues within 4Å: Chain C: F.339, V.340, R.424 Chain D: V.273, W.276 Ligands: PX4.35, PIO.41 Ligand excluded by PLIP PX4.44: 4 residues within 4Å: Chain D: F.446, I.450, Y.451, L.454 Ligand excluded by PLIP PX4.45: 4 residues within 4Å: Chain D: S.329, A.336 Ligands: PX4.46, PX4.55 Ligand excluded by PLIP PX4.46: 5 residues within 4Å: Chain D: L.325, F.326, I.431, C.435 Ligands: PX4.45 Ligand excluded by PLIP PX4.48: 4 residues within 4Å: Chain E: F.446, I.450, Y.451, L.454 Ligand excluded by PLIP PX4.49: 4 residues within 4Å: Chain E: S.329, A.336 Ligands: PX4.12, PX4.50 Ligand excluded by PLIP PX4.50: 5 residues within 4Å: Chain E: L.325, F.326, I.431, C.435 Ligands: PX4.49 Ligand excluded by PLIP PX4.55: 7 residues within 4Å: Chain D: F.339, V.340, R.424 Chain E: V.273, W.276 Ligands: PX4.45, 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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