4XPB: Transporter

X-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) bound to cocaine. Determined by X-ray diffraction at 3.05 Å resolution. Released 13 May 2015.

Method: X-ray diffraction
Resolution: 3.05 Å
Organisms: Drosophila melanogaster, Mus musculus
Chains: 3
Atoms: 7,471
Mol. weight: 111.65 kDa
Ligands: CLR, COC
Released: 13 May 2015

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

Secondary structure: helices and β-sheets

4XPB contains 50 α-helices and 48 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: 41 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	108-120	13
α-helix	125-136	12
β-strand	157-158	2	1
β-strand	209-210	2	1
α-helix	211-215	5
α-helix	216-221	6
α-helix	223-225	3
β-strand	235	1	2
α-helix	237-254	18
α-helix	258-268	11
α-helix	270-284	15
α-helix	289-297	9
α-helix	301-304	4
α-helix	307-320	14
α-helix	327-332	6
α-helix	341-372	32
α-helix	378-381	4
α-helix	386-387	2
α-helix	388-392	5
α-helix	393-397	5
α-helix	403-436	34
α-helix	438-441	4
α-helix	444-459	16
β-strand	464	1	2
α-helix	467-477	11
α-helix	481-492	12
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	552-553	2
α-helix	554-568	15
α-helix	570-581	12
α-helix	586-593	8

Chain H: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
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	78-83	6	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
β-strand	123	1	13
β-strand	126-130	5	14
β-strand	141-151	11	14
β-strand	152	1	13
β-strand	157-160	4	15
β-strand	169-177	9	14
β-strand	180-190	11	14
β-strand	200-205	6	15
α-helix	206-208	3
β-strand	210-215	6	15

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	19-29	11	4
β-strand	34-39	6	5
β-strand	45-50	6	5
β-strand	54-55	2	5
β-strand	63-76	14	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	146-149	4	8
β-strand	150-151	2	9
β-strand	154-155	2	9
β-strand	160-164	5	7
α-helix	166-168	3
β-strand	174-183	10	7
α-helix	184-188	5
β-strand	192-198	7	8
β-strand	206-211	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transporter	A	protein	543	Drosophila melanogaster	Q7K4Y6 (AlphaFold model)
Antibody fragment heavy chain-protein, 9D5-heavy chain	L	protein	214	Mus musculus
Antibody fragment light chain-protein, 9D5-light chain	H	protein	240	Mus musculus

Sequence of entity 1 (A), FASTA

>4XPB_1 Transporter (chains A)
MNSISDERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIP
LFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVGFYYNVIIAWSLRFFFASF
TNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALC
LLIVYLICYFSLWKGISTSGKVVWFTALFPYAVLLILLIRGLTLPGSFLGIQYYLTPNFS
AIYKAEVWVDAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFV
IFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSS
FGGMEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYS
ILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYGLIGY
EPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQL
VPR

Sequence of entity 2 (L), FASTA

>4XPB_2 Antibody fragment heavy chain-protein, 9D5-heavy chain (chains L)
ENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVP
ARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 3 (H), FASTA

>4XPB_3 Antibody fragment light chain-protein, 9D5-light chain (chains H)
MNFGLRLVFLVLILKGVQCEVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSP
EKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEV
RQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWN
SGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
COC	Cocaine	C17 H21 N 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

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