SMTL ID : 7li7.1

apo serotonin transporter reconstituted in lipid nanodisc in presence of 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: 4 residues within 4Å: Chain A: N.127, G.129, N.130, H.145 No protein-ligand interaction detected (PLIP)

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

D12.2: 3 residues within 4Å: Chain A: Y.107, I.110, L.183 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.110, A:L.183 D12.6: 3 residues within 4Å: Chain A: F.113, I.354 Ligands: HP6.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.354 D12.10: 6 residues within 4Å: Chain A: T.44, I.48, Y.280, L.284, C.291, F.458 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.48, A:I.48, A:L.284, A:F.458, A:F.458

5 x HP6: HEPTANE(Non-covalent)

HP6.3: 1 residues within 4Å: Chain A: T.404 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.404 HP6.4: 3 residues within 4Å: Chain A: L.167, V.410, L.499 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.410, A:L.499 HP6.5: 2 residues within 4Å: Chain A: W.495, I.498 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.495, A:I.498 HP6.7: 2 residues within 4Å: Chain A: I.173, L.400 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.173, A:L.400 HP6.9: 3 residues within 4Å: Chain A: L.358 Ligands: D12.6, LNK.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.358

1 x LNK: PENTANE(Non-covalent)

LNK.8: 3 residues within 4Å: Chain A: V.187, F.190 Ligands: HP6.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.187, A:F.190

1 x CLR: CHOLESTEROL(Non-covalent)

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

1 x D10: DECANE(Non-covalent)

D10.12: 4 residues within 4Å: Chain A: R.386, A.390, I.393, F.397 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.386, A:I.393, A:F.397

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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