SMTL ID : 7li6.1

apo SERT reconstituted in lipid nanodisc in KCl

Coordinates

PDB Format Compare

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: 5 residues within 4Å: Chain A: G.129, N.130, H.145, T.147, E.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.145

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

CL.2: 4 residues within 4Å: Chain A: Y.43, Q.254, S.258, S.294 Ligand excluded by PLIP

1 x R16: HEXADECANE(Non-covalent)

R16.3: 3 residues within 4Å: Chain A: I.48, I.52, C.291 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.52

9 x HP6: HEPTANE(Non-covalent)(Non-functional Binders)

HP6.4: 1 residues within 4Å: Chain A: V.464 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.464 HP6.6: 2 residues within 4Å: Chain A: V.219, A.222 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.219, A:A.222 HP6.9: 4 residues within 4Å: Chain A: F.185, T.186, Y.189, F.396 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.185, A:Y.189, A:F.396 HP6.10: 2 residues within 4Å: Chain A: I.393, T.394 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.393 HP6.11: 2 residues within 4Å: Chain A: I.89, V.372 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.89, A:V.372 HP6.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.15: 1 residues within 4Å: Chain A: Y.85 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.85 HP6.17: 1 residues within 4Å: Chain A: A.516 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.516 HP6.20: 2 residues within 4Å: Chain A: F.49, F.470 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.49, A:F.49, A:F.470

6 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.5: 1 residues within 4Å: Chain A: F.299 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.299 D10.14: 3 residues within 4Å: Chain A: V.401, L.414, L.499 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.401, A:L.414, A:L.499 D10.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.22: 1 residues within 4Å: Chain A: I.173 No protein-ligand interaction detected (PLIP) D10.23: 1 residues within 4Å: Chain A: W.436 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.436 D10.25: 3 residues within 4Å: Chain A: L.479, T.505 Ligands: D12.24 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.479

3 x D12: DODECANE(Non-covalent)

D12.7: 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 D12.8: 2 residues within 4Å: Chain A: L.179, L.183 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.183 D12.24: 3 residues within 4Å: Chain A: I.498, T.505 Ligands: D10.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.498, A:T.505

4 x LNK: PENTANE(Non-functional Binders)(Non-covalent)(Covalent)

LNK.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LNK.16: 1 residues within 4Å: Chain A: A.516 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.516 LNK.18: 2 residues within 4Å: Chain A: F.473, C.476 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.473 LNK.19: 2 residues within 4Å: Chain A: L.243, W.248 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.248, A:W.248

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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