SMTL ID : 6dg8.1

Full-length 5-HT3A receptor in a serotonin-bound conformation- State 2

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(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.75 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.141, K.190, Y.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.190 NAG-NAG.5: 1 residues within 4Å: Chain B: N.75 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.141, K.190, Y.206 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.190 NAG-NAG.8: 1 residues within 4Å: Chain C: N.75 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.141, K.190, Y.206 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.190 NAG-NAG.11: 3 residues within 4Å: Chain D: P.70, D.74, N.75 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain D: R.168, F.186, K.190, Y.206 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.190 NAG-NAG.14: 1 residues within 4Å: Chain E: N.75 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain E: N.141, K.190, Y.206 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.190

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: 2 residues within 4Å: Chain A: N.157, I.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 3 residues within 4Å: Chain B: I.153, N.157, I.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 2 residues within 4Å: Chain C: N.157, I.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 2 residues within 4Å: Chain D: N.157, I.158 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 1 residues within 4Å: Chain E: N.157 No protein-ligand interaction detected (PLIP)

5 x SRO: SEROTONIN(Non-covalent)

SRO.16: 9 residues within 4Å: Chain A: T.147, W.149, F.192, I.194, Y.200 Chain E: W.56, Y.57, R.58, Y.119 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:W.149, A:W.149, A:Y.200, E:W.56, E:Y.119 Hydrogen bonds: A:T.147, A:T.147 SRO.17: 10 residues within 4Å: Chain B: W.56, Y.57, R.58, Y.119 Chain C: T.147, S.148, W.149, F.192, I.194, Y.200 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.149, C:W.149, C:F.192, C:F.192, B:W.56, B:W.56 Hydrogen bonds: C:T.147, C:S.148, B:Y.57 pi-Stacking: B:Y.119 SRO.18: 9 residues within 4Å: Chain A: W.56, Y.57, R.58, Y.119 Chain B: T.147, W.149, F.192, I.194, Y.200 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.56, B:W.149, B:W.149, B:Y.200 Hydrogen bonds: A:W.56, B:T.147, B:T.147 pi-Stacking: A:Y.119 SRO.19: 10 residues within 4Å: Chain C: W.56, Y.57, R.58, Y.119 Chain D: T.147, S.148, W.149, F.192, I.194, Y.200 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.149, D:W.149, D:F.192, D:F.192, D:Y.200, C:W.56, C:W.56 Hydrogen bonds: D:T.147, D:S.148, C:Y.57 pi-Stacking: C:Y.119 SRO.20: 10 residues within 4Å: Chain D: W.56, Y.57, R.58, Y.119 Chain E: T.147, S.148, W.149, F.192, I.194, Y.200 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:W.56, E:W.149, E:W.149, E:F.192, E:F.192 Hydrogen bonds: D:Y.57, E:T.147, E:S.148 pi-Stacking: D:Y.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basak, S. et al., Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT3Areceptor. Nature (2018)

Release Date

2018-11-07

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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