SMTL ID : 8de4.1

Native serotonin transporter in complex with 15B8 Fab in the presence of methamphetamine

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: 5 residues within 4Å: Chain A: T.128, G.129, N.130, H.145 Chain B: Y.101 No protein-ligand interaction detected (PLIP)

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

CL.2: 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.3: 4 residues within 4Å: Chain A: A.18, N.23, S.258, N.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.18, A:D.20, A:N.23, A:N.290 NA.4: 5 residues within 4Å: Chain A: G.16, V.19, T.355, L.356, D.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.359, A:D.359

1 x B40: (2S)-N-methyl-1-phenylpropan-2-amine(Non-covalent)

B40.5: 10 residues within 4Å: Chain A: Y.17, A.18, D.20, I.94, F.257, S.258, G.260, F.263, S.360, G.364 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.17, A:I.94, A:F.263, A:F.263 Hydrogen bonds: A:D.20

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 7 residues within 4Å: Chain A: I.48, Y.280, L.284, V.288, F.295, F.458, W.459 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.48, A:L.284, A:L.284, A:V.288, A:F.295, A:F.458, A:W.459 Hydrogen bonds: A:Y.280 Y01.7: 6 residues within 4Å: Chain A: K.7, V.8, L.12, I.15, Y.211, V.289 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.12, A:Y.211, A:V.289

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.8: 10 residues within 4Å: Chain A: D.250, E.416, F.417, G.420, P.421, F.478, S.481, Y.501, T.505, F.508 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.417, A:Y.501, A:Y.501, A:F.508, A:F.508 Hydrogen bonds: A:D.250, A:D.250, A:E.416, A:S.481, A:S.481

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, D. et al., Native serotonin transporter in complex with 15B8 Fab in the presence of methamphetamine. To be published

Release Date

2023-07-05

Peptides

Transporter: A
15B8 Fab heavy chain variable domain: B
15B8 Fab light chain variable domain: 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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Transporter

15B8 Fab heavy chain variable domain

15B8 Fab light chain variable domain

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