SMTL ID : 6hiq.1

Mouse serotonin 5-HT3 receptor, serotonin-bound, I2 conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

10 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: 5 residues within 4Å: Chain A: I.152, N.156, I.157, T.158, F.188 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.140, Q.187, Y.205, I.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.187 NAG-NAG.3: 5 residues within 4Å: Chain B: I.152, N.156, I.157, T.158, F.188 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.140, Q.187, Y.205, I.207 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.187 NAG-NAG.5: 5 residues within 4Å: Chain C: I.152, N.156, I.157, T.158, F.188 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: N.140, Q.187, Y.205, I.207 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.187 NAG-NAG.7: 5 residues within 4Å: Chain D: I.152, N.156, I.157, T.158, F.188 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: N.140, Q.187, Y.205, I.207 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.187 NAG-NAG.9: 5 residues within 4Å: Chain E: I.152, N.156, I.157, T.158, F.188 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain E: N.140, Q.187, Y.205, I.207 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.187

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

NAG.11: 2 residues within 4Å: Chain A: D.73, N.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.74 NAG.13: 2 residues within 4Å: Chain B: D.73, N.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.74 NAG.15: 2 residues within 4Å: Chain C: D.73, N.74 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.74 NAG.17: 2 residues within 4Å: Chain D: D.73, N.74 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.74 NAG.19: 2 residues within 4Å: Chain E: D.73, N.74 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.74

5 x SRO: SEROTONIN(Non-covalent)

SRO.12: 10 residues within 4Å: Chain A: N.93, T.146, S.147, W.148, I.193, Y.199 Chain B: W.55, Y.56, Y.118, K.119 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.55, B:Y.118, A:W.148 Hydrogen bonds: B:Y.56, B:Y.56, B:K.119, A:N.93, A:T.146 SRO.14: 10 residues within 4Å: Chain B: N.93, T.146, S.147, W.148, I.193, Y.199 Chain E: W.55, Y.56, Y.118, K.119 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:W.55, E:Y.118, B:W.148 Hydrogen bonds: E:Y.56, E:Y.56, E:K.119, B:N.93, B:T.146 SRO.16: 8 residues within 4Å: Chain A: W.55, Y.56 Chain C: N.93, T.146, S.147, W.148, I.193, Y.199 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:W.148, A:W.55, A:W.55 Hydrogen bonds: C:N.93, C:T.146, A:Y.56, A:Y.56 SRO.18: 10 residues within 4Å: Chain C: W.55, Y.56, Y.118, K.119 Chain D: N.93, T.146, S.147, W.148, I.193, Y.199 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.55, C:W.55, C:Y.118, D:W.148 Hydrogen bonds: C:Y.56, C:Y.56, C:K.119, D:N.93, D:T.146 SRO.20: 10 residues within 4Å: Chain D: W.55, Y.56, Y.118, K.119 Chain E: N.93, T.146, S.147, W.148, I.193, Y.199 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:W.148, D:W.55, D:Y.118 Hydrogen bonds: E:N.93, E:T.146, D:Y.56, D:Y.56, D:K.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Polovinkin, L. et al., Conformational transitions of the serotonin 5-HT3receptor. Nature (2018)

Release Date

2018-11-07

Peptides

5-hydroxytryptamine receptor 3A: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
B

D
C

E
D

Membrane

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