SMTL ID : 7li9.1

5-HT bound serotonin transporter reconstituted in lipid nanodisc in KCl

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.130, H.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.145

2 x D12: DODECANE(Non-covalent)

D12.2: 3 residues within 4Å: Chain A: L.106, F.113, I.354 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.106, A:F.113, A:I.354 D12.3: 3 residues within 4Å: Chain A: I.110, L.179, L.183 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.110, A:L.183, A:L.183

2 x HP6: HEPTANE(Non-covalent)

HP6.4: 2 residues within 4Å: Chain A: A.390, T.394 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.390 HP6.5: 2 residues within 4Å: Chain A: L.170, I.173 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.170, A:I.173

3 x D10: DECANE(Non-covalent)(Covalent)

D10.6: 4 residues within 4Å: Chain A: L.167, V.401, L.414, L.499 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.401, A:L.414, A:L.414, A:L.499 D10.8: 2 residues within 4Å: Chain A: I.48, W.459 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.48, A:W.459 D10.9: 2 residues within 4Å: Chain A: I.173, A.178 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.178

1 x LNK: PENTANE(Non-covalent)

LNK.7: 1 residues within 4Å: Chain A: Y.85 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.85

2 x SRO: SEROTONIN(Non-covalent)

SRO.10: 9 residues within 4Å: Chain A: D.20, A.91, I.94, Y.98, F.257, F.263, S.360, T.361, G.364 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.91, A:I.94, A:I.94 Hydrogen bonds: A:F.257 SRO.11: 9 residues within 4Å: Chain A: I.249, D.250, E.416, Y.417, P.421, F.478, S.481, P.483, Y.501 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.416, A:Y.417, A:P.421, A:P.483, A:Y.501 Hydrogen bonds: A:D.250 pi-Stacking: A:F.478

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

CL.12: 4 residues within 4Å: Chain A: Y.43, Q.254, S.258, S.294 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, D. et al., Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv (2021)

Release Date

2021-12-15

Peptides

Sodium-dependent serotonin transporter: A
variable domain of 15B8 antibody Fab heavy chain: B
variable domain of 15B8 antibody Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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

variable domain of 15B8 antibody Fab heavy chain

variable domain of 15B8 antibody Fab light chain

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