SMTL ID : 7mgw.1

5-HT bound serotonin transporter reconstituted in lipid nanodisc in NaCl in occluded conformation

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 No protein-ligand interaction detected (PLIP)

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

CL.2: 6 residues within 4Å: Chain A: N.23, F.27, Y.43, Q.254, I.255, S.294 Ligand excluded by PLIP

4 x D12: DODECANE(Non-covalent)(Covalent)

D12.3: 1 residues within 4Å: Chain A: F.113 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.113 D12.6: 3 residues within 4Å: Chain A: I.48, Y.280, C.291 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.48 D12.8: 3 residues within 4Å: Chain A: Y.107, L.179, L.183 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.179, A:L.183, A:L.183 D12.9: 2 residues within 4Å: Chain A: I.173, F.396 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.173, A:F.396

1 x LNK: PENTANE(Non-functional Binders)

LNK.4: 1 residues within 4Å: Ligands: HP6.5 No protein-ligand interaction detected (PLIP)

6 x HP6: HEPTANE(Non-functional Binders)(Covalent)(Non-covalent)

HP6.5: 1 residues within 4Å: Ligands: LNK.4 No protein-ligand interaction detected (PLIP) HP6.10: 4 residues within 4Å: Chain A: L.170, L.400, V.401, F.405 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.170, A:L.400, A:F.405 HP6.11: 1 residues within 4Å: Ligands: HP6.14 No protein-ligand interaction detected (PLIP) HP6.12: 2 residues within 4Å: Chain A: I.498, L.499 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.498, A:L.499 HP6.14: 2 residues within 4Å: Ligands: HP6.11, HP6.15 No protein-ligand interaction detected (PLIP) HP6.15: 1 residues within 4Å: Ligands: HP6.14 No protein-ligand interaction detected (PLIP)

1 x D10: DECANE(Non-covalent)

D10.7: 2 residues within 4Å: Chain A: W.495, L.499 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.495, A:L.499

2 x SRO: SEROTONIN(Non-covalent)

SRO.13: 10 residues within 4Å: Chain A: Y.17, D.20, A.91, I.94, A.95, F.257, F.263, S.360, T.361, G.364 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.91, A:I.94, A:A.95, A:F.257 Hydrogen bonds: A:Y.17, A:F.257 SRO.16: 8 residues within 4Å: Chain A: D.250, E.416, Y.417, P.421, F.478, S.481, P.483, Y.501 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.421, A:P.483, A:Y.501 Hydrogen bonds: A:D.250

1 x CLR: CHOLESTEROL(Covalent)

CLR.17: 6 residues within 4Å: Chain A: V.8, L.11, L.12, I.15, Y.211, V.289 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.11, A:L.12, A:I.15, A:V.289

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 antiboty 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 antiboty Fab light chain

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