5I71: Ts3 human serotonin transporter

X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at the central site. Determined by X-ray diffraction at 3.15 Å resolution. Released 13 Apr 2016.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 7,616
Mol. weight: 110.55 kDa
Ligands: 68P, NAG, CLR, D12
Released: 13 Apr 2016

Explore 5I71 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I71 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: 39 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	85-96	12
α-helix	99-110	12
α-helix	114-117	4
α-helix	118-124	7
α-helix	125-129	5
α-helix	130-143	14
α-helix	149-152	4
α-helix	156-159	4
α-helix	160-172	13
α-helix	176-187	12
β-strand	209	1	1
β-strand	225	1	1
α-helix	227-231	5
α-helix	232-236	5
α-helix	239-241	3
β-strand	251	1	2
α-helix	253-265	13
α-helix	281-284	4
α-helix	287-301	15
α-helix	306-313	8
α-helix	323-337	15
α-helix	343-349	7
α-helix	358-389	32
α-helix	394-397	4
α-helix	404	1
α-helix	405-410	6
α-helix	411-415	5
α-helix	420-453	34
β-strand	455	1	3
β-strand	458	1	3
α-helix	462-476	15
β-strand	482	1	2
α-helix	485-491	7
α-helix	492-496	5
α-helix	497-514	18
α-helix	518-528	11
α-helix	532-534	3
α-helix	535-539	5
α-helix	540-544	5
α-helix	545-558	14
α-helix	560-563	4
β-strand	564	1	4
β-strand	569	1	4
α-helix	570-571	2
α-helix	574-583	10
α-helix	588-599	12
α-helix	604-612	9

Chain B: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	5
β-strand	29-31	3	6
β-strand	37-44	8	5
β-strand	52-58	7	7
β-strand	64-71	8	7
β-strand	76-79	4	7
β-strand	87-92	6	5
β-strand	97-102	6	5
α-helix	107-109	3
β-strand	112-118	7	7
β-strand	127-128	2	7
β-strand	132-133	2	7
β-strand	134-136	3	6
α-helix	142-144	3
β-strand	145-149	5	8
α-helix	150-152	3
β-strand	160-170	11	8
β-strand	176-179	4	9
β-strand	188-196	9	8
β-strand	199-209	11	8
β-strand	219-224	6	9
β-strand	229-234	6	9

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	10
β-strand	30-34	5	11
β-strand	39-44	6	10
β-strand	53-58	6	11
β-strand	65-69	5	11
β-strand	73-74	2	11
α-helix	75	1
β-strand	82-86	5	10
β-strand	90-95	6	10
α-helix	100-102	3
β-strand	105-110	6	11
α-helix	116	1
β-strand	118	1	11
β-strand	122-127	6	11
β-strand	131	1	12
β-strand	134-138	5	13
α-helix	139-141	3
α-helix	142-147	6
β-strand	149-159	11	13
β-strand	160	1	12
β-strand	165-169	5	14
β-strand	174-175	2	14
β-strand	179-183	5	13
α-helix	184-187	4
β-strand	193-202	10	13
α-helix	203-206	4
β-strand	211-217	7	14
α-helix	224	1
β-strand	225-230	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent serotonin transporter	A	protein	549	Homo sapiens	P31645 (AlphaFold model)
8B6 antibody, heavy chain	B	protein	221	Mus musculus
8B6 antibody, light chain	C	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>5I71_1 Sodium-dependent serotonin transporter (chains A)
GSQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICAQNGGGAFLLPYTIMAIFGGIPLF
YMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTD
QLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISW
QLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIALSVLLVRGATLPGAWRGVLFYL
KPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSF
VSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLIT
LGLDSSFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLE
EYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFII
ASFLMSPPQLRLFQYNYPYWSIILGYAIGTSSFICIPTYIAYRLIITPGTFKERIIKSIT
PETPTLVPR

Sequence of entity 2 (B), FASTA

>5I71_2 8B6 antibody, heavy chain (chains B)
EVQLQQSGPELVKPGASVKISCKASGYTFTDYYMNWVKQSHGKSLEWIGNINPNNGGTSY
NQKFKGKATLTVDKSSTTAYMELRSLTSEDSAVYYCTRSPVRPYYFDYWGQGTTLTVSSA
KTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGL
YTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGP

Sequence of entity 3 (C), FASTA

>5I71_3 8B6 antibody, light chain (chains C)
DIVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKPGQSPKLLIYSASYRYTGVPD
RFTGSGSGTDFTFTISSVQAEDLAVYYCQQHYSIPRTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
68P	(1S)-1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-…	C20 H21 F N2 O	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CLR	Cholesterol	C27 H46 O	1
D12	Dodecane	C12 H26	1
HEX	Hexane	C6 H14	1

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

Primary citation

X-ray structures and mechanism of the human serotonin transporter. Coleman, J.A., Green, E.M., Gouaux, E. Nature (2016) 532:334-339. DOI 10.1038/nature17629 · PubMed

Other PDB entries of the same protein (UniProt P31645 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9HCO 2.78 Å, Outward-open structure of human serotonin transporter bound to vilazodone
7TXT 3.0 Å, Structure of human serotonin transporter bound to small molecule '8090 in lipid nanodisc…
5I6X 3.14 Å, X-ray structure of the ts3 human serotonin transporter complexed with paroxetine at the…
9VWS 3.2 Å, Cryo-EM structure of human serotonin transporter in complex with tesofensine
5I73 3.24 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…
9IY7 3.27 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with S-ketamine
6VRH 3.3 Å, Cryo-EM structure of the wild-type human serotonin transporter complexed with paroxetine…
7LIA 3.3 Å, 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in…
5I74 3.4 Å, X-ray structure of the ts3 human serotonin transporter complexed with Br-citalopram at…
9PNS 3.4 Å, Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc…
5I75 3.49 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…
7LI6 3.5 Å, apo SERT reconstituted in lipid nanodisc in KCl

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