SMTL ID : 6m38.1

X-ray structure of a Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) in S-duloxetine bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 29E: (3S)-N-methyl-3-(naphthalen-1-yloxy)-3-(thiophen-2-yl)propan-1-amine(Non-covalent)

29E.1: 14 residues within 4Å: Chain A: F.19, A.20, D.22, A.93, V.96, Y.99, Y.100, F.254, S.255, F.260, S.356, S.357, G.360 Ligands: NA.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.19, A:A.93, A:V.96, A:Y.100, A:F.260, A:F.260 Hydrogen bonds: A:F.254

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 10 residues within 4Å: Chain A: L.49, A.50, I.54, Y.277, F.285, S.288, F.292, G.451, Y.453, W.454 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.49, A:A.50, A:I.54, A:F.285, A:F.285, A:F.292, A:Y.453, A:W.454 Hydrogen bonds: A:G.451

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

NA.3: 6 residues within 4Å: Chain A: A.20, D.22, N.25, S.255, N.287 Ligands: 29E.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.22, A:N.25, A:N.287 NA.5: 7 residues within 4Å: Chain A: G.18, F.19, V.21, D.22, L.352, D.355, S.356 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.355, A:S.356

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

CL.4: 5 residues within 4Å: Chain A: F.29, Y.45, Q.251, S.255, S.291 Ligand excluded by PLIP

1 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.6: 9 residues within 4Å: Chain A: R.109, F.112, A.113, T.116, P.120, Y.154, D.173, L.176, I.180 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.112, A:D.173, A:I.180 Hydrogen bonds: A:R.109, A:R.109, A:A.113, A:Y.154 Salt bridges: A:R.109

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 6 residues within 4Å: Chain A: I.17, L.205, Y.208, L.211, L.212, I.286 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.17, A:L.205, A:Y.208, A:Y.208, A:L.211, A:L.212, A:I.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pidathala, S. et al., Structural basis of norepinephrine recognition and transport inhibition in neurotransmitter transporters. Nat Commun (2021)

Release Date

2021-02-17

Peptides

Sodium-dependent dopamine transporter: A
Antibody fragment 9D5 light chain: B
Antibody fragment 9D5 heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

Membrane

We predict this structure to be a membrane protein.
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Sodium-dependent dopamine transporter

Antibody fragment 9D5 light chain

Antibody fragment 9D5 heavy chain

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