SMTL ID : 6m3z.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 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: 5 residues within 4Å: Chain A: R.109, F.112, A.113, Y.154, D.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.109, A:F.112, A:D.173, A:D.173 GLC-GLC.2: 5 residues within 4Å: Chain A: Y.277, F.448 Chain C: Q.103, R.104 Ligands: Y01.9 No protein-ligand interaction detected (PLIP)

1 x F0F: (1R,2S)-2-(aminomethyl)-N,N-diethyl-1-phenyl-cyclopropane-1-carboxamide(Non-covalent)

F0F.3: 13 residues within 4Å: Chain A: F.19, A.20, D.22, V.96, Y.99, Y.100, F.254, S.255, G.257, F.260, S.356, G.360 Ligands: NA.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.96, A:Y.100, A:Y.100, A:F.254, A:F.260 Hydrogen bonds: A:S.255

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: D.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.410

1 x D10: DECANE(Non-covalent)

D10.5: 2 residues within 4Å: Chain A: Y.95, C.497 No protein-ligand interaction detected (PLIP)

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

CL.6: 4 residues within 4Å: Chain A: Y.45, Q.251, S.255, S.291 Ligand excluded by PLIP

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

NA.7: 5 residues within 4Å: Chain A: A.20, D.22, N.25, S.255 Ligands: F0F.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.25 NA.8: 5 residues within 4Å: Chain A: G.18, V.21, L.352, D.355, S.356 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.356, A:S.356

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.9: 9 residues within 4Å: Chain A: G.46, L.49, A.50, Y.277, F.285, G.451, Y.453, W.454 Ligands: GLC-GLC.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.49, A:A.50, A:F.285, A:Y.453, A:W.454 Hydrogen bonds: A:G.451

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.10: 6 residues within 4Å: Chain A: L.13, L.14, L.205, Y.208, L.212, I.286 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.13, A:L.14, A:L.205, 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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