4XP6: Drosophila dopamine transporter

X-ray structure of Drosophila dopamine transporter bound to psychostimulant methamphetamine. Determined by X-ray diffraction at 3.1 Å resolution. Released 13 May 2015.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Drosophila melanogaster, Mus musculus
Chains: 3
Atoms: 7,582
Mol. weight: 108.36 kDa
Ligands: B40, NAG, CLR, Y01
Released: 13 May 2015

Explore 4XP6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XP6 contains 50 α-helices and 51 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 40 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	33-44	12
α-helix	48-51	4
α-helix	53-59	7
α-helix	62-65	4
α-helix	66-72	7
α-helix	73-77	5
α-helix	78-91	14
α-helix	95-102	8
α-helix	104-106	3
α-helix	108-123	16
α-helix	125-137	13
α-helix	144-146	3
β-strand	158	1	1
β-strand	210	1	1
α-helix	211-215	5
α-helix	216-221	6
β-strand	235	1	2
α-helix	237-254	18
α-helix	258-268	11
α-helix	271-284	14
α-helix	289-297	9
α-helix	303-305	3
α-helix	307-320	14
α-helix	327-333	7
α-helix	341-373	33
α-helix	378-381	4
α-helix	386-387	2
α-helix	388-392	5
α-helix	393-399	7
α-helix	403-436	34
α-helix	439-442	4
α-helix	445-459	15
β-strand	464	1	2
α-helix	467-477	11
α-helix	482-492	11
α-helix	493-497	5
α-helix	500-511	12
α-helix	514-516	3
α-helix	517-521	5
α-helix	522-526	5
α-helix	527-540	14
β-strand	546-547	2	3
β-strand	550-551	2	3
α-helix	554-568	15
α-helix	570-577	8
α-helix	588-593	6

Chain H: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	9
β-strand	34-39	6	5
β-strand	45-51	7	5
β-strand	58-60	3	5
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	5
β-strand	108-109	2	5
β-strand	113-115	3	5
β-strand	116-117	2	10
α-helix	120-122	3
β-strand	123	1	11
β-strand	126-130	5	12
β-strand	141-151	11	12
β-strand	152	1	11
β-strand	157-160	4	13
β-strand	169-171	3	12
α-helix	172-174	3
β-strand	175-176	2	12
β-strand	181-190	10	12
β-strand	200	1	14
β-strand	201-205	5	13
α-helix	206-208	3
β-strand	210-212	3	13
β-strand	215	1	14

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	19-25	7	4
β-strand	34-39	6	5
β-strand	46-49	4	5
β-strand	55	1	5
β-strand	63-68	6	4
β-strand	71-76	6	4
α-helix	81-83	3
β-strand	86-91	6	5
α-helix	97	1
β-strand	98-99	2	5
β-strand	103-107	5	5
β-strand	112	1	6
β-strand	115-119	5	7
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	7
β-strand	141	1	6
β-strand	146-151	6	8
β-strand	154-155	2	8
β-strand	160-164	5	7
α-helix	165-168	4
β-strand	174-183	10	7
α-helix	184-187	4
β-strand	192-198	7	8
β-strand	206-211	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transporter	A	protein	534	Drosophila melanogaster	Q7K4Y6 (AlphaFold model)
Antibody fragment heavy chain-protein, 9D5-heavy chain	L	protein	213	Mus musculus
Antibody fragment light chain-protein, 9D5-light chain	H	protein	219	Mus musculus

Sequence of entity 1 (A), FASTA

>4XP6_1 Transporter (chains A)
DERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYME
LALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLP
WTSCNNIWNTPNCRPFEGHVEGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLI
VYLICYFSLWKGISTSGKVVWFTALFPYAVLLILLIRGLTLPGSFLGIQYYLTPNFSAIY
KAEVWVDAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFS
VLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGG
SEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILV
AVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYGLIGYEPL
TYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRD

Sequence of entity 2 (L), FASTA

>4XP6_2 Antibody fragment heavy chain-protein, 9D5-heavy chain (chains L)
ENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVP
ARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 3 (H), FASTA

>4XP6_3 Antibody fragment light chain-protein, 9D5-light chain (chains H)
EVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRLEWVAEISSGGRYIYY
SDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEVRQRGFDYWGQGTTLTVSSA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Ligands and cofactors

ID	Name	Formula	Copies
B40	(2S)-N-methyl-1-phenylpropan-2-amine	C10 H15 N	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
CLR	Cholesterol	C27 H46 O	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	1

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

Neurotransmitter and psychostimulant recognition by the dopamine transporter. Wang, K.H., Penmatsa, A., Gouaux, E. Nature (2015) 521:322-327. DOI 10.1038/nature14431 · PubMed

Other PDB entries of the same protein (UniProt Q7K4Y6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7WGT 2.75 Å, X-ray structure of thermostabilized Drosophila dopamine transporter with GABA…
4XP4 2.8 Å, X-ray structure of Drosophila dopamine transporter in complex with cocaine
4XP9 2.8 Å, X-ray structure of Drosophila dopamine transporter bound to psychostimulant D-amphetamine
6M2R 2.8 Å, X-ray structure of a functional Drosophila dopamine transporter in L-norepinephrine…
6M0Z 2.88 Å, X-ray structure of Drosophila dopamine transporter with NET-like mutations…
4XP1 2.89 Å, X-ray structure of Drosophila dopamine transporter bound to neurotransmitter dopamine
4XPH 2.9 Å, X-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M)…
7WLW 2.9 Å, X-ray structure of thermostabilized Drosophila dopamine transporter with GABA…
4XPA 2.95 Å, X-ray structure of Drosophila dopamine transporter bound to 3,4dichlorophenethylamine
4M48 2.96 Å, X-ray structure of dopamine transporter elucidates antidepressant mechanism
4XNU 2.98 Å, X-ray structure of Drosophila dopamine transporter in complex with nisoxetine
4XNX 3.0 Å, X-ray structure of Drosophila dopamine transporter in complex with reboxetine

Browse structure collections

About this viewer

MolViewer shows 4XP6 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.