SMTL ID : 8aw2.1

Mouse serotonin 5-HT3A receptor in complex with vortioxetine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.268, I.269, T.270, F.300 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: N.268, I.269, T.270, F.300 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain C: N.268, I.269, T.270, F.300 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain D: N.268, I.269, T.270, F.300 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain E: N.268, I.269, T.270, F.300 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: N.252, Y.317, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.252, Y.317, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.252, Y.317, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: N.252, Y.317, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain E: N.252, Y.317, I.319 No protein-ligand interaction detected (PLIP)

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.11: 2 residues within 4Å: Chain A: D.185, N.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.186 NAG.14: 2 residues within 4Å: Chain B: D.185, N.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.186 NAG.17: 2 residues within 4Å: Chain C: D.185, N.186 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.186 NAG.20: 2 residues within 4Å: Chain D: D.185, N.186 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.186 NAG.23: 2 residues within 4Å: Chain E: D.185, N.186 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.186

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

5 x VTX: Vortioxetine(Non-covalent)

VTX.13: 10 residues within 4Å: Chain A: N.205, W.260, I.305, Y.311 Chain E: I.148, W.167, R.169, Y.230, R.273, I.284 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:I.148, E:W.167, E:R.169, E:Y.230, E:I.284, A:W.260, A:I.305, A:I.305 pi-Stacking: E:Y.230 VTX.16: 10 residues within 4Å: Chain A: I.148, W.167, R.169, Y.230, R.273, I.284 Chain B: N.205, W.260, I.305, Y.311 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.260, B:I.305, B:I.305, A:I.148, A:W.167, A:R.169, A:Y.230, A:I.284 pi-Stacking: A:Y.230 VTX.19: 10 residues within 4Å: Chain B: I.148, W.167, R.169, Y.230, R.273, I.284 Chain C: N.205, W.260, I.305, Y.311 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.148, B:W.167, B:R.169, B:Y.230, B:I.284, C:W.260, C:I.305, C:I.305 pi-Stacking: B:Y.230 VTX.22: 11 residues within 4Å: Chain C: I.148, W.167, R.169, Y.230, R.273, D.281, I.284 Chain D: N.205, W.260, I.305, Y.311 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:W.260, D:I.305, D:I.305, C:I.148, C:W.167, C:R.169, C:Y.230, C:I.284 pi-Stacking: C:Y.230 VTX.25: 10 residues within 4Å: Chain D: I.148, W.167, R.169, Y.230, R.273, I.284 Chain E: N.205, W.260, I.305, Y.311 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:I.148, D:W.167, D:R.169, D:Y.230, D:I.284, E:W.260, E:I.305, E:I.305 pi-Stacking: D:Y.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Sanchez, U. et al., Structural determinants for activity of the antidepressant vortioxetine at human and rodent 5-HT 3 receptors. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-03-06

Peptides

5-hydroxytryptamine receptor 3A: 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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5-hydroxytryptamine receptor 3A