SMTL ID : 6y1z.1

Mouse serotonin 5HT3 receptor in complex with palonosetron

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: 3 residues within 4Å: Chain A: N.268, T.270, F.300 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.300 NAG-NAG-BMA.3: 3 residues within 4Å: Chain B: N.268, T.270, F.300 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.300 NAG-NAG-BMA.5: 3 residues within 4Å: Chain C: N.268, T.270, F.300 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.300 NAG-NAG-BMA.7: 3 residues within 4Å: Chain D: N.268, T.270, F.300 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.300 NAG-NAG-BMA.9: 3 residues within 4Å: Chain E: N.268, T.270, F.300 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.300

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: 4 residues within 4Å: Chain A: N.252, Q.299, Y.317, I.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.299 NAG-NAG.4: 4 residues within 4Å: Chain B: N.252, Q.299, Y.317, I.319 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.299 NAG-NAG.6: 4 residues within 4Å: Chain C: N.252, Q.299, Y.317, I.319 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.299 NAG-NAG.8: 4 residues within 4Å: Chain D: N.252, Q.299, Y.317, I.319 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.299 NAG-NAG.10: 4 residues within 4Å: Chain E: N.252, Q.299, Y.317, I.319 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.299

5 x TRP: TRYPTOPHAN(Non-covalent)

TRP.11: 6 residues within 4Å: Chain A: F.248, P.324, L.559, W.560, I.562 Ligands: HIS.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.248, A:P.324, H.12 Hydrogen bonds: A:I.562 TRP.15: 6 residues within 4Å: Chain B: F.248, P.324, L.559, W.560, I.562 Ligands: HIS.16 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain B Hydrophobic interactions: H.16, B:F.248, B:P.324 Hydrogen bonds: B:I.562 TRP.19: 6 residues within 4Å: Chain C: F.248, P.324, L.559, W.560, I.562 Ligands: HIS.20 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:F.248, C:P.324, H.20 Hydrogen bonds: C:I.562 TRP.24: 6 residues within 4Å: Chain D: F.248, P.324, L.559, W.560, I.562 Ligands: HIS.25 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.248, D:P.324, H.25 Hydrogen bonds: D:I.562 TRP.28: 6 residues within 4Å: Chain E: F.248, P.324, L.559, W.560, I.562 Ligands: HIS.29 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:F.248, E:P.324, H.29 Hydrogen bonds: E:I.562

5 x HIS: HISTIDINE(Non-covalent)

HIS.12: 4 residues within 4Å: Chain A: W.560, S.561, I.562 Ligands: TRP.11 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrophobic interactions: W.11 Hydrogen bonds: A:W.560 HIS.16: 4 residues within 4Å: Chain B: W.560, S.561, I.562 Ligands: TRP.15 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrophobic interactions: W.15 Hydrogen bonds: B:W.560 HIS.20: 4 residues within 4Å: Chain C: W.560, S.561, I.562 Ligands: TRP.19 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain C Hydrophobic interactions: W.19 Hydrogen bonds: C:W.560 HIS.25: 4 residues within 4Å: Chain D: W.560, S.561, I.562 Ligands: TRP.24 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain D Hydrophobic interactions: W.24 Hydrogen bonds: D:W.560 HIS.29: 4 residues within 4Å: Chain E: W.560, S.561, I.562 Ligands: TRP.28 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Ligand interactions Hydrogen bonds: E:W.560 Hydrophobic interactions: W.28

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

NAG.13: 2 residues within 4Å: Chain A: D.185, N.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.185, A:N.186 NAG.17: 2 residues within 4Å: Chain B: D.185, N.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.185, B:N.186 NAG.21: 2 residues within 4Å: Chain C: D.185, N.186 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.185, C:N.186 NAG.26: 2 residues within 4Å: Chain D: D.185, N.186 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.185, D:N.186 NAG.30: 2 residues within 4Å: Chain E: D.185, N.186 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.185, E:N.186

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.14: 8 residues within 4Å: Chain A: D.146, I.148, W.167, R.169, Y.230 Chain C: N.205, W.260, Y.311 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.148, A:I.148, A:W.167, A:W.167, A:R.169 O7B.18: 8 residues within 4Å: Chain B: D.146, I.148, W.167, R.169, Y.230 Chain E: N.205, W.260, Y.311 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.148, B:I.148, B:W.167, B:W.167, B:R.169 O7B.22: 8 residues within 4Å: Chain C: D.146, I.148, W.167, R.169, Y.230 Chain D: N.205, W.260, Y.311 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.148, C:W.167, C:W.167, C:R.169 O7B.23: 8 residues within 4Å: Chain B: N.205, W.260, Y.311 Chain D: D.146, I.148, W.167, R.169, Y.230 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.148, D:W.167, D:W.167, D:R.169 O7B.27: 8 residues within 4Å: Chain A: N.205, W.260, Y.311 Chain E: D.146, I.148, W.167, R.169, Y.230 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.148, E:W.167, E:W.167, E:R.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarkadas, E. et al., The Binding of Palonosetron and Other Antiemetic Drugs to the Serotonin 5-HT3 Receptor. Structure (2020)

Release Date

2020-03-04

Peptides

5-hydroxytryptamine receptor 3A: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

E
E

Membrane

We predict this structure to be a membrane protein.
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5-hydroxytryptamine receptor 3A

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