SMTL ID : 9euo.1

Outward-open structure of Drosophila dopamine transporter bound to an atypical non-competitive inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x 01: N-[3-(6-chloranyl-1,3,4,9-tetrahydropyrido[3,4-b]indol-2-yl)propyl]butanamide

01.1: 21 residues within 4Å: Chain A: F.24, R.33, V.94, I.97, A.98, V.101, Y.104, Y.105, T.253, Q.254, F.257, F.263, V.265, S.359, G.363, D.413, A.417, G.418, I.421, L.476 Ligands: 144.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.101, A:V.101, A:F.257, A:F.263, A:F.263, A:A.417 Hydrogen bonds: A:Y.104

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 15 residues within 4Å: Chain A: Y.50, G.51, L.54, A.55, I.59, P.60, Y.280, L.284, F.288, S.291, A.292, F.295, G.454, Y.456, W.457 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.54, A:L.54, A:A.55, A:I.59, A:F.288, A:F.288, A:A.292, A:F.295, A:W.457, A:W.457 Hydrogen bonds: A:G.454, A:W.457

1 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.3: 14 residues within 4Å: Chain A: F.24, A.25, V.26, D.27, A.29, Y.105, F.257, S.258, L.259, G.260, F.263, S.359 Ligands: 01.1, NA.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.24, A:D.27, A:D.27 Salt bridges: A:D.27

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 12 residues within 4Å: Chain A: V.15, L.18, L.19, I.22, L.208, Y.211, L.214, L.215, L.218, L.285, I.289, I.296 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.18, A:L.19, A:I.22, A:L.208, A:L.215, A:I.289, A:I.296

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

NA.5: 7 residues within 4Å: Chain A: A.25, V.26, D.27, N.30, S.258, N.290 Ligands: 144.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.25, A:N.30, A:N.290

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

CL.6: 8 residues within 4Å: Chain A: N.30, F.34, Y.50, Q.254, S.258, N.290, S.291, S.294 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedersen, C.N. et al., Cryo-EM structure of the dopamine transporter with a novel atypical non-competitive inhibitor bound to the orthosteric site. J.Neurochem. (2024)

Release Date

2024-07-24

Peptides

Sodium-dependent dopamine transporter: A
9D5 ANTIBODY, LIGHT CHAIN: B
9D5 ANTIBODY, 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

9D5 ANTIBODY, LIGHT CHAIN

9D5 ANTIBODY, HEAVY CHAIN

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