SMTL ID : 6m47.1

X-ray structure of a Drosophila dopamine transporter with NET-like mutations (D121G/S426M/F471L) in tramadol bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 3 residues within 4Å: Chain A: R.109, Y.154, D.173 No protein-ligand interaction detected (PLIP) GLC-GLC.2: 4 residues within 4Å: Chain A: E.157, I.170, W.172, Q.400 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.157, A:Q.400

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 4 residues within 4Å: Chain A: L.205, L.212, I.286, I.293 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.205, A:L.212, A:I.286, A:I.286, A:I.293

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 8 residues within 4Å: Chain A: A.50, I.54, Y.277, F.285, G.451, R.452, Y.453, W.454 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.50, A:I.54, A:F.285, A:Y.453, A:W.454, A:W.454 Hydrogen bonds: A:G.451

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

NA.5: 4 residues within 4Å: Chain A: A.20, N.25, S.255, N.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.25, A:N.25, A:N.287 NA.6: 6 residues within 4Å: Chain A: G.18, V.21, T.351, L.352, D.355, S.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.351, A:D.355, A:S.356

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

CL.7: 4 residues within 4Å: Chain A: Y.45, Q.251, S.255, S.291 Ligand excluded by PLIP

1 x F1U: (1S,2S)-2-[(dimethylamino)methyl]-1-(3-methoxyphenyl)cyclohexan-1-ol(Non-covalent)

F1U.8: 8 residues within 4Å: Chain A: F.19, D.22, A.93, Y.100, F.254, F.260, S.356, G.360 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.100, A:F.260 Salt bridges: A:D.22 pi-Stacking: A:Y.100

1 x D10: DECANE(Non-covalent)

D10.9: 1 residues within 4Å: Chain A: F.94 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.94

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 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 Heavy chain

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