SMTL ID : 8fsb.1

Full-length mouse 5-HT3A receptor in complex with serotonin, open-like

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: D.156, N.157 Chain B: R.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.109 NAG.2: 3 residues within 4Å: Chain A: N.223, Y.288, I.290 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.290 NAG.3: 5 residues within 4Å: Chain A: I.235, N.239, I.240, T.241, F.271 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain B: D.156, N.157 Chain C: R.109 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.109 NAG.7: 3 residues within 4Å: Chain B: N.223, Y.288, I.290 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.290 NAG.8: 5 residues within 4Å: Chain B: I.235, N.239, I.240, T.241, F.271 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain C: D.156, N.157 Chain D: R.109 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.109 NAG.11: 3 residues within 4Å: Chain C: N.223, Y.288, I.290 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.290 NAG.12: 5 residues within 4Å: Chain C: I.235, N.239, I.240, T.241, F.271 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain D: D.156, N.157 Chain E: R.109 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.109 NAG.15: 3 residues within 4Å: Chain D: N.223, Y.288, I.290 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.290 NAG.16: 5 residues within 4Å: Chain D: I.235, N.239, I.240, T.241, F.271 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain A: R.109 Chain E: D.156, N.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.109 NAG.19: 3 residues within 4Å: Chain E: N.223, Y.288, I.290 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.290 NAG.20: 5 residues within 4Å: Chain E: I.235, N.239, I.240, T.241, F.271 No protein-ligand interaction detected (PLIP)

5 x SRO: SEROTONIN(Non-covalent)

SRO.4: 9 residues within 4Å: Chain A: S.230, W.231, I.276, Y.282 Chain E: W.138, Y.139, R.140, Y.201, K.202 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:W.138, E:W.138 Hydrogen bonds: E:Y.139, E:Y.139, E:K.202, A:S.230 pi-Stacking: E:Y.201 SRO.5: 9 residues within 4Å: Chain A: W.138, Y.139, R.140, Y.201, K.202 Chain B: S.230, W.231, I.276, Y.282 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.138, A:W.138 Hydrogen bonds: A:Y.139, A:Y.139, A:K.202, B:S.230 pi-Stacking: A:Y.201 SRO.9: 9 residues within 4Å: Chain B: W.138, Y.139, R.140, Y.201, K.202 Chain C: S.230, W.231, I.276, Y.282 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.138, B:W.138 Hydrogen bonds: B:Y.139, B:Y.139, B:K.202, C:S.230 pi-Stacking: B:Y.201 SRO.13: 9 residues within 4Å: Chain C: W.138, Y.139, R.140, Y.201, K.202 Chain D: S.230, W.231, I.276, Y.282 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:S.230, C:Y.139, C:Y.139, C:K.202 Hydrophobic interactions: C:W.138, C:W.138 pi-Stacking: C:Y.201 SRO.17: 9 residues within 4Å: Chain D: W.138, Y.139, R.140, Y.201, K.202 Chain E: S.230, W.231, I.276, Y.282 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:W.138, D:W.138 Hydrogen bonds: D:Y.139, D:Y.139, D:K.202, E:S.230 pi-Stacking: D:Y.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Felt, K. et al., Structural basis for partial agonism in 5-HT 3A receptors. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-12-27

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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