SMTL ID : 7lia.1

5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in outward facing conformation

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: 3 residues within 4Å: Chain A: G.129, N.130, H.145 No protein-ligand interaction detected (PLIP)

2 x SRO: SEROTONIN(Non-covalent)

SRO.2: 10 residues within 4Å: Chain A: Y.17, D.20, A.91, I.94, A.95, Y.98, F.263, S.360, T.361, G.364 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.91, A:I.94, A:A.95 SRO.6: 7 residues within 4Å: Chain A: E.416, Y.417, P.421, F.478, S.481, P.483, Y.501 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.417, A:P.421, A:P.483, A:Y.501, A:Y.501 Hydrogen bonds: A:S.481

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

CL.3: 5 residues within 4Å: Chain A: F.27, Y.43, Q.254, S.258, S.294 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: A.18, D.20, N.23, S.258, N.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.20, A:N.23, A:N.290, A:N.290 NA.5: 4 residues within 4Å: Chain A: G.16, V.19, L.356, D.359 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.16

5 x D10: DECANE(Non-covalent)

D10.7: 5 residues within 4Å: Chain A: T.44, I.48, Y.280, C.291, W.459 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.44, A:I.48, A:W.459 D10.19: 4 residues within 4Å: Chain A: Y.107, I.110, Q.176, L.183 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.176, A:L.183 D10.20: 6 residues within 4Å: Chain A: F.185, T.186, Y.189, L.389, V.392, I.393 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.185, A:Y.189, A:Y.189, A:L.389, A:I.393 D10.24: 5 residues within 4Å: Chain A: L.170, F.397, V.401, T.404 Ligands: HP6.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.397, A:V.401, A:T.404 D10.25: 4 residues within 4Å: Chain A: Y.494, I.498, Y.501 Ligands: HP6.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.498, A:Y.501, A:Y.501

13 x HP6: HEPTANE(Non-covalent)

HP6.8: 1 residues within 4Å: Chain A: L.235 No protein-ligand interaction detected (PLIP) HP6.9: 2 residues within 4Å: Chain A: L.218, V.231 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.231 HP6.10: 4 residues within 4Å: Chain A: V.187, F.190, S.191, V.202 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.190, A:F.190, A:V.202 HP6.11: 3 residues within 4Å: Chain A: A.390, I.393, T.394 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.390 HP6.12: 3 residues within 4Å: Chain A: L.479, Y.501 Ligands: D10.25 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.501 HP6.13: 2 residues within 4Å: Chain A: V.401 Ligands: D10.24 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.401 HP6.14: 4 residues within 4Å: Chain A: I.173, W.175, M.182, F.396 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.175, A:F.396 HP6.15: 5 residues within 4Å: Chain A: L.167, L.170, V.410, W.495, L.499 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.170, A:V.410, A:V.410, A:W.495, A:L.499 HP6.16: 3 residues within 4Å: Chain A: T.513, A.516, Y.517 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.513, A:A.516, A:Y.517 HP6.17: 1 residues within 4Å: Chain A: I.520 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.520 HP6.21: 3 residues within 4Å: Chain A: W.495, L.499 Ligands: LNK.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.495, A:W.495, A:L.499 HP6.22: 4 residues within 4Å: Chain A: C.88, I.89, V.372, F.376 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.89, A:V.372, A:F.376 HP6.23: 1 residues within 4Å: Chain A: F.387 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.387

1 x LNK: PENTANE(Non-covalent)

LNK.18: 2 residues within 4Å: Chain A: C.502 Ligands: HP6.21 No protein-ligand interaction detected (PLIP)

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.26: 9 residues within 4Å: Chain A: V.8, L.11, L.12, I.15, Y.211, L.214, S.215, V.289, V.296 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.8, A:L.12, A:I.15, A:Y.211, A:Y.211, A:V.296, A:V.296

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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