SMTL ID : 6w1m.1

Cryo-EM structure of 5HT3A receptor in presence of Ondansetron

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.76 NAG-NAG.4: 1 residues within 4Å: Chain B: N.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.76 NAG-NAG.7: 1 residues within 4Å: Chain C: N.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.76 NAG-NAG.10: 1 residues within 4Å: Chain D: N.76 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.76 NAG-NAG.13: 1 residues within 4Å: Chain E: N.76 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.76

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.2: 4 residues within 4Å: Chain A: N.158, I.159, T.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain B: N.158, I.159, T.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain C: N.158, I.159, T.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain D: N.158, I.159, T.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain E: N.158, I.159, T.160, F.190 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.3: 3 residues within 4Å: Chain A: N.142, Y.207, I.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.207 NAG-NAG.6: 3 residues within 4Å: Chain B: N.142, Y.207, I.209 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.207 NAG-NAG.9: 3 residues within 4Å: Chain C: N.142, Y.207, I.209 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.207 NAG-NAG.12: 3 residues within 4Å: Chain D: N.142, Y.207, I.209 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.207 NAG-NAG.15: 3 residues within 4Å: Chain E: N.142, Y.207, I.209 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.207

5 x S87: ondansetron(Non-covalent)

S87.16: 10 residues within 4Å: Chain A: N.95, S.149, W.150, I.195, Y.201 Chain E: D.36, I.38, W.57, R.59, Y.120 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:I.195, E:I.38, E:W.57, E:W.57, E:R.59 Hydrogen bonds: A:N.95 pi-Stacking: A:W.150, E:Y.120 S87.17: 10 residues within 4Å: Chain A: D.36, I.38, W.57, R.59, Y.120 Chain B: N.95, S.149, W.150, I.195, Y.201 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.38, A:I.38, A:W.57, A:R.59, B:I.195 Hydrogen bonds: B:N.95 pi-Stacking: B:W.150 S87.18: 11 residues within 4Å: Chain B: D.36, I.38, W.57, R.59, Y.120, R.163 Chain C: N.95, S.149, W.150, I.195, Y.201 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.195, B:I.38, B:I.38, B:W.57 Hydrogen bonds: C:N.95 pi-Stacking: C:W.150 pi-Cation interactions: B:R.59 S87.19: 11 residues within 4Å: Chain C: D.36, I.38, W.57, R.59, Y.120, R.163 Chain D: N.95, S.149, W.150, I.195, Y.201 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.195, C:I.38, C:I.38, C:W.57, C:R.59 Hydrogen bonds: D:N.95 pi-Stacking: D:W.150 pi-Cation interactions: C:R.59 S87.20: 10 residues within 4Å: Chain D: D.36, I.38, W.57, R.59, Y.120 Chain E: N.95, S.149, W.150, I.195, Y.201 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:I.195, D:I.38, D:I.38, D:W.57, D:W.57, D:R.59 Hydrogen bonds: E:N.95 pi-Stacking: E:W.150, D:Y.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basak, S. et al., High-resolution structures of multiple 5-HT 3A R-setron complexes reveal a novel mechanism of competitive inhibition. Elife (2020)

Release Date

2021-01-13

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

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