SMTL ID : 8frx.1

Full-length mouse 5-HT3A receptor in complex with SMP100, pre-activated

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x Y82: 5-[(1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl]-1,3,4,5-tetrahydro-6H-azepino[5,4,3-cd]indazol-6-one(Non-covalent)

Y82.1: 12 residues within 4Å: Chain A: N.176, S.230, W.231, F.274, I.276, D.277, Y.282 Chain E: D.117, I.119, W.138, R.140, Y.201 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:I.119, E:W.138, E:W.138, E:R.140, A:F.274, A:Y.282 Y82.5: 12 residues within 4Å: Chain A: D.117, I.119, W.138, R.140, Y.201 Chain B: N.176, S.230, W.231, F.274, I.276, D.277, Y.282 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.274, B:Y.282, A:I.119, A:W.138, A:W.138, A:R.140 Y82.9: 12 residues within 4Å: Chain B: D.117, I.119, W.138, R.140, Y.201 Chain C: N.176, S.230, W.231, F.274, I.276, D.277, Y.282 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.119, B:W.138, B:W.138, B:R.140, C:F.274, C:Y.282 Y82.13: 12 residues within 4Å: Chain C: D.117, I.119, W.138, R.140, Y.201 Chain D: N.176, S.230, W.231, F.274, I.276, D.277, Y.282 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.119, C:W.138, C:W.138, C:R.140, D:F.274, D:Y.282 Y82.17: 12 residues within 4Å: Chain D: D.117, I.119, W.138, R.140, Y.201 Chain E: N.176, S.230, W.231, F.274, I.276, D.277, Y.282 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:F.274, E:Y.282, D:I.119, D:W.138, D:W.138, D:R.140

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

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

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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