SMTL ID : 6m2r.1

X-ray structure of a functional Drosophila dopamine transporter in L-norepinephrine bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

DMU.1: 7 residues within 4Å: Chain A: R.109, F.112, A.113, P.120, Y.154, D.173, L.176 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:D.173 Hydrogen bonds: A:R.109, A:R.109, A:A.113, A:Y.154 Salt bridges: A:R.109

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

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

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 7 residues within 4Å: Chain A: V.10, L.13, I.17, L.205, Y.208, L.212, I.286 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.13, A:I.17, A:L.205, A:Y.208, A:Y.208, A:L.212, A:I.286, A:I.286

1 x LNR: L-NOREPINEPHRINE(Non-covalent)

LNR.4: 11 residues within 4Å: Chain A: F.19, D.22, A.93, V.96, D.97, Y.100, F.254, S.255, F.260, S.356, G.360 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.96, A:Y.100, A:F.260 Hydrogen bonds: A:D.97, A:F.254

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

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

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

NA.6: 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:A.20, A:N.25, A:N.287 NA.7: 6 residues within 4Å: Chain A: G.18, V.21, D.22, L.352, D.355, S.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.355, A:S.356, A:S.356 NA.11: 4 residues within 4Å: Chain B: Q.6, A.9, S.101, G.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.101 NA.12: 5 residues within 4Å: Chain B: Q.6, S.7, M.21, T.22, T.103 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.6, B:S.7, B:T.103, B:T.103

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

D10.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.9: 3 residues within 4Å: Chain A: A.508, V.509, F.512 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.508, A:V.509, A:V.509, A:F.512, A:F.512, A:F.512 D10.10: 1 residues within 4Å: Chain A: G.473 No protein-ligand interaction detected (PLIP)

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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