4XP9: Drosophila dopamine transporter

X-ray structure of Drosophila dopamine transporter bound to psychostimulant D-amphetamine. Determined by X-ray diffraction at 2.8 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Drosophila melanogaster, Mus musculus
Chains: 3
Atoms: 7,665
Mol. weight: 109.73 kDa
Ligands: Y01, NAG, MPO, CLR
Released: 6 May 2015

Explore 4XP9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XP9 contains 57 α-helices and 50 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 C: 42 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	33-44	12
α-helix	47-51	5
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	108-136	29
α-helix	144-146	3
β-strand	158	1	1
β-strand	210	1	1
α-helix	211-214	4
α-helix	215-220	6
α-helix	223-225	3
β-strand	235	1	2
α-helix	237-254	18
α-helix	258-284	27
α-helix	289-297	9
α-helix	301-305	5
α-helix	307-320	14
α-helix	327-332	6
α-helix	341-369	29
α-helix	370-374	5
α-helix	378-381	4
α-helix	386-387	2
α-helix	388-392	5
α-helix	393-398	6
α-helix	403-436	34
α-helix	438-442	5
α-helix	444-459	16
α-helix	460-463	4
β-strand	464	1	2
α-helix	467-477	11
α-helix	480-492	13
α-helix	493-499	7
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	570-579	10
α-helix	586-593	8
α-helix	597-600	4

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	9
β-strand	6-7	2	10
β-strand	11-12	2	11
β-strand	19-23	5	10
β-strand	25	1	9
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	69-73	5	10
β-strand	78-82	5	10
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	108-109	2	12
β-strand	113-115	3	12
β-strand	116-117	2	11
α-helix	120-122	3
β-strand	123	1	13
α-helix	124-125	2
β-strand	126-130	5	14
α-helix	131-133	3
β-strand	141-151	11	14
β-strand	152	1	13
β-strand	157-160	4	15
α-helix	161-163	3
β-strand	169-176	8	14
β-strand	181-190	10	14
β-strand	200-205	6	15
α-helix	206-208	3
β-strand	210-215	6	15

Chain L: 8 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
α-helix	31-33	3
β-strand	34-39	6	5
β-strand	46-50	5	5
β-strand	54-55	2	5
α-helix	56	1
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	145-151	7	8
β-strand	154-156	3	8
β-strand	160-164	5	7
α-helix	165-168	4
β-strand	174-183	10	7
α-helix	184-188	5
β-strand	192-199	8	8
β-strand	202-211	10	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transporter	C	protein	541	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 (C), FASTA

>4XP9_1 Transporter (chains C)
DERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYME
LALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLP
WTSCNNIWNTPNCRPFEGHVEGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLI
VYLICYFSLWKGISTSGKVVWFTALFPYAVLLILLIRGLTLPGSFLGIQYYLTPNFSAIY
KAEVWVDAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFS
VLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGG
SEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILV
AVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYGLIGYEPL
TYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQLLVP
R

Sequence of entity 2 (L), FASTA

>4XP9_2 ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN (chains L)
ENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVP
ARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIEGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 3 (H), FASTA

>4XP9_3 ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN (chains H)
EVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRLEWVAEISSGGRYIYY
SDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEVRQRGFDYWGQGTTLTVSSA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Ligands and cofactors

ID	Name	Formula	Copies
Y01	Cholesterol hemisuccinate	C31 H50 O4	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MPO	3[N-morpholino]propane sulfonic acid	C7 H15 N O4 S	1
CLR	Cholesterol	C27 H46 O	1
1WE	(2S)-1-phenylpropan-2-amine	C9 H13 N	1
P4G	1-ethoxy-2-(2-ethoxyethoxy)ethane	C8 H18 O3	2

Water and common crystallization additives (NA, CL) 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
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
9EUP 3.0 Å, Inhibitor-free outward-open structure of Drosophila dopamine transporter

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