SMTL ID : 6w1y.1

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

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 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.142, Y.207, I.209 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.142, Y.207, I.209 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain D: N.142, Y.207, I.209 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain E: N.142, Y.207, I.209 No protein-ligand interaction detected (PLIP)

5 x O7B: (3~{a}~{S})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~{H}-benzo[de]isoquinolin-1-one(Non-covalent)

O7B.16: 9 residues within 4Å: Chain A: N.95, W.150, I.195, Y.201 Chain E: I.38, W.57, Y.58, R.59, Y.120 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:W.150, A:I.195, A:I.195, A:Y.201, E:I.38, E:W.57, E:R.59 O7B.17: 8 residues within 4Å: Chain A: I.38, W.57, R.59, Y.120 Chain B: N.95, W.150, I.195, Y.201 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.38, A:R.59, B:W.150, B:I.195, B:I.195, B:Y.201 O7B.18: 8 residues within 4Å: Chain B: I.38, W.57, R.59, Y.120 Chain C: N.95, W.150, I.195, Y.201 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.150, C:I.195, C:I.195, C:Y.201, B:I.38, B:R.59 O7B.19: 9 residues within 4Å: Chain C: D.36, I.38, W.57, R.59, Y.120 Chain D: N.95, W.150, I.195, Y.201 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.150, D:I.195, D:I.195, D:Y.201, C:I.38, C:R.59 O7B.20: 9 residues within 4Å: Chain D: I.38, W.57, Y.58, R.59, Y.120 Chain E: N.95, W.150, I.195, Y.201 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:W.150, E:I.195, E:I.195, E:Y.201, D:I.38, D:R.59

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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