SMTL ID : 7lwd.1

Cryo-EM structure of the wild-type human serotonin transporter complexed with vilazodone, imipramine and 15B8 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x IXX: 3-(5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE(Non-covalent)

IXX.1: 13 residues within 4Å: Chain A: Y.19, A.20, D.22, A.93, I.96, Y.99, F.259, S.260, F.265, S.362, G.366, T.421 Ligands: YG7.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.19, A:A.93, A:I.96, A:I.96, A:F.265, A:F.265, A:T.421 Salt bridges: A:D.22

1 x YG7: 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide(Non-covalent)

YG7.2: 15 residues within 4Å: Chain A: D.22, G.24, R.28, Q.256, F.259, E.418, T.421, P.423, F.480, S.483, P.485, G.502, Y.503, G.506 Ligands: IXX.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.259, A:F.259, A:E.418, A:P.423, A:Y.503 Hydrogen bonds: A:D.22, A:G.24, A:S.483 pi-Stacking: A:F.480 pi-Cation interactions: A:R.28, A:R.28

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.3: 3 residues within 4Å: Chain A: N.129, N.132, H.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.129, A:N.132, A:H.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plenge, P. et al., The antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter. Nat Commun (2021)

Release Date

2021-08-11

Peptides

Sodium-dependent serotonin transporter: A
heavy chain antibody fragment: B
light chain antibody fragment: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Membrane

We predict this structure to be a membrane protein.
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Sodium-dependent serotonin transporter

heavy chain antibody fragment

light chain antibody fragment

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