SMTL ID : 8vby.1

Structure of the human dopamine transporter in complex with beta-CFT, MRS7292 and divalent zinc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x 42L: methyl (1R,2S,3S,5S)-3-(4-fluorophenyl)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate(Non-covalent)

42L.1: 9 residues within 4Å: Chain A: F.26, D.29, N.32, V.102, Y.106, G.273, F.276, S.372, G.376 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.26, A:V.102, A:Y.106, A:Y.106, A:F.276, A:F.276 Water bridges: A:A.31 Salt bridges: A:D.29 pi-Stacking: A:F.276

1 x 01: methyl (1S,2R,3S,4R,5R)-4-{2-[(5-chlorothiophen-2-yl)ethynyl]-6-(methylamino)-9H-purin-9-yl}-2,3-dihydroxybicyclo[3.1.0]hexane-1-carboxylate

01.2: 17 residues within 4Å: Chain A: L.30, A.31, V.33, W.34, I.109, L.230, V.313, V.314, K.334, D.335, G.336, L.339, I.340, I.343, Y.344, M.364, F.422 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.30, A:V.33, A:I.340, A:Y.344 Hydrogen bonds: A:K.334, A:G.336 pi-Stacking: A:W.34, A:W.34, A:W.34, A:Y.344

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.138

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 6 residues within 4Å: Chain A: F.104, I.180, D.181, F.412, V.421, L.510 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.104, A:F.412, A:V.421, A:L.510 Y01.10: 7 residues within 4Å: Chain A: I.17, L.20, T.221, Y.224, V.225, T.228, I.302 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.17, A:L.20, A:T.221, A:Y.224, A:V.225, A:I.302 Y01.11: 12 residues within 4Å: Chain A: L.49, L.53, M.56, V.57, M.61, Y.293, T.300, S.301, S.304, L.305, Y.469, W.470 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.49, A:V.57, A:T.300, A:L.305, A:Y.469, A:W.470 Hydrogen bonds: A:Y.293 Y01.38: 7 residues within 4Å: Chain A: L.200, F.203, S.204, W.206, T.211, V.215 Ligands: D12.39 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.211, A:V.215

8 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.5: 2 residues within 4Å: Chain A: H.394, F.401 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.401 D10.7: 3 residues within 4Å: Chain A: I.490, W.512, M.519 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.490, A:W.512 D10.18: 1 residues within 4Å: Chain A: A.192 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.192 D10.24: 1 residues within 4Å: Chain A: L.400 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.400 D10.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

7 x LNK: PENTANE(Non-functional Binders)(Non-covalent)

LNK.6: 1 residues within 4Å: Ligands: LNK.21 No protein-ligand interaction detected (PLIP) LNK.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LNK.9: 1 residues within 4Å: Chain A: L.248 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.248 LNK.21: 2 residues within 4Å: Chain A: F.388 Ligands: LNK.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.388 LNK.22: 2 residues within 4Å: Chain A: L.384 Ligands: LNK.23 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.384 LNK.23: 2 residues within 4Å: Chain A: L.390 Ligands: LNK.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.390 LNK.32: 1 residues within 4Å: Chain A: L.408 No protein-ligand interaction detected (PLIP)

8 x HP6: HEPTANE(Non-covalent)(Non-functional Binders)

HP6.12: 1 residues within 4Å: Chain A: I.490 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.490 HP6.15: 2 residues within 4Å: Chain A: G.46, V.250 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.250 HP6.19: 1 residues within 4Å: Chain A: V.522 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.522 HP6.20: 1 residues within 4Å: Chain A: I.524 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.524 HP6.27: 2 residues within 4Å: Chain A: K.214, W.217 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.214, A:W.217 HP6.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.37: 1 residues within 4Å: Chain A: F.118 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.118

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 4 residues within 4Å: Chain A: D.141, H.143, H.325, E.346 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.141, A:D.141, A:H.143, A:H.325, A:E.346

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

NA.14: 6 residues within 4Å: Chain A: G.25, V.28, D.29, L.368, D.371, S.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.29, A:D.371, A:S.372

6 x D12: DODECANE(Non-covalent)

D12.16: 2 residues within 4Å: Chain A: V.225, W.357 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.225, A:W.357 D12.17: 1 residues within 4Å: Chain A: F.121 No protein-ligand interaction detected (PLIP) D12.26: 1 residues within 4Å: Chain A: F.203 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.203 D12.28: 1 residues within 4Å: Chain A: L.305 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.305 D12.36: 1 residues within 4Å: Chain A: V.360 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.360 D12.39: 2 residues within 4Å: Chain A: L.200 Ligands: Y01.38 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.200

1 x MYS: PENTADECANE(Non-covalent)

MYS.25: 5 residues within 4Å: Chain A: V.195, V.199, Y.202, L.400, V.403 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.195, A:V.199, A:Y.202, A:Y.202, A:L.400, A:V.403

2 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.29: 1 residues within 4Å: Chain A: L.231 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.231 OCT.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srivastava, D.K. et al., Structure of the human dopamine transporter and mechanisms of inhibition. Nature (2024)

Release Date

2024-08-07

Peptides

Sodium-dependent dopamine transporter: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

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