SMTL ID : 6be1.1

Cryo-EM structure of serotonin receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

2 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: 4 residues within 4Å: Chain A: N.159, I.160, T.161, F.191 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.191 NAG-NAG-BMA.6: 5 residues within 4Å: Chain C: T.33, N.159, I.160, T.161, F.191 No protein-ligand interaction detected (PLIP)

8 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.143, F.188, Y.208, I.210 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.77 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.143, F.188, Y.208, I.210 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: E.73, N.77 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain D: N.143, F.188, Q.190, K.192, Y.208 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.188 NAG-NAG.10: 5 residues within 4Å: Chain E: N.159, I.160, T.161, F.191 Ligands: BMA.24 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.191 NAG-NAG.11: 1 residues within 4Å: Chain E: N.77 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: N.143, F.188, Q.190, Y.208 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 3 residues within 4Å: Chain B: N.159, T.161, F.191 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.8: 5 residues within 4Å: Chain D: I.155, N.159, I.160, T.161, F.191 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: N.77 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Ligands: NAG.13 No protein-ligand interaction detected (PLIP) NAG.18: 4 residues within 4Å: Chain C: N.143, Y.208, I.210 Ligands: NAG.19 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.210 Hydrogen bonds: C:N.143 NAG.19: 3 residues within 4Å: Chain C: F.188, Q.190 Ligands: NAG.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.190 NAG.22: 3 residues within 4Å: Chain D: E.73, D.76, N.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.73, D:N.77

1 x NA: SODIUM ION(Non-functional Binders)

NA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

5 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.16: 6 residues within 4Å: Chain A: F.298, R.301, L.302 Chain E: C.238, R.430, F.433 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:R.430, E:R.430 Salt bridges: A:R.301 PX4.17: 6 residues within 4Å: Chain A: C.238, R.430, F.433 Chain B: F.298, R.301, L.302 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.430 Salt bridges: B:R.301 PX4.21: 6 residues within 4Å: Chain B: C.238, R.430, F.433 Chain C: F.298, R.301, L.302 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.430 Salt bridges: B:R.430, C:R.301 PX4.23: 5 residues within 4Å: Chain C: R.430, F.433 Chain D: F.298, R.301, L.302 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.430 Salt bridges: D:R.301 PX4.25: 4 residues within 4Å: Chain D: R.430 Chain E: F.298, R.301, L.302 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.430, D:R.430 Salt bridges: E:R.301

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.24: 1 residues within 4Å: Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basak, S. et al., Cryo-EM structure of 5-HT. Nat Commun (2018)

Release Date

2018-02-07

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