9PNS: Human serotonin transporter

Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc and NaCl. Determined by electron microscopy at 3.4 Å resolution. Released 4 Mar 2026.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 6,049
Mol. weight: 86.38 kDa
Ligands: A1CIZ
Released: 4 Mar 2026

Explore 9PNS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PNS contains 46 α-helices and 35 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: 42 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	86-96	11
α-helix	99	1
α-helix	100-104	5
α-helix	105-111	7
α-helix	115-124	10
α-helix	125-129	5
α-helix	130-143	14
α-helix	146-149	4
α-helix	150-153	4
α-helix	156-159	4
α-helix	160-188	29
α-helix	196-198	3
β-strand	209	1	1
β-strand	225	1	1
α-helix	227-230	4
α-helix	231-236	6
α-helix	239-241	3
β-strand	244	1	2
β-strand	247	1	2
β-strand	251	1	3
α-helix	253-270	18
α-helix	274-276	3
α-helix	277-284	8
α-helix	287-301	15
α-helix	305-311	7
α-helix	317-319	3
α-helix	326-336	11
α-helix	343-348	6
α-helix	357-390	34
α-helix	405	1
α-helix	406-410	5
α-helix	411-414	4
α-helix	422-451	30
α-helix	455-458	4
α-helix	462-477	16
α-helix	478-481	4
β-strand	482	1	3
α-helix	485-495	11
α-helix	499-510	12
α-helix	511-515	5
α-helix	518-529	12
α-helix	536-539	4
α-helix	540-544	5
α-helix	545-558	14
β-strand	564-565	2	4
β-strand	568-569	2	4
α-helix	570-571	2
α-helix	573-584	12
α-helix	588-599	12
α-helix	604-609	6

Chain B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	5
β-strand	29	1	6
β-strand	38-42	5	5
α-helix	48-50	3
β-strand	53-58	6	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
β-strand	112-113	2	7
β-strand	116-117	2	7
α-helix	121-123	3
β-strand	129	1	7
β-strand	134-135	2	7
β-strand	136	1	6

Chain C: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	8
β-strand	30-31	2	9
α-helix	33-34	2
β-strand	39-44	6	8
β-strand	50-51	2	10
β-strand	54-55	2	10
β-strand	57-62	6	11
α-helix	67-68	2
β-strand	69-73	5	11
β-strand	77-78	2	11
β-strand	86	1	8
β-strand	89-91	3	8
β-strand	94-99	6	8
β-strand	109-114	6	11
β-strand	121-122	2	11
β-strand	127-128	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent serotonin transporter	A	protein	541	Homo sapiens	P31645 (AlphaFold model)
15B8 Fab heavy chain	B	protein	120	Mus musculus
15B8 Fab light chain	C	protein	111	Mus musculus

Sequence of entity 1 (A), FASTA

>9PNS_1 Sodium-dependent serotonin transporter (chains A)
GERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYME
LALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLP
WTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLA
LCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPN
WQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSG
FVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGL
DSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYA
TGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSF
LMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPET
P

Sequence of entity 2 (B), FASTA

>9PNS_2 15B8 Fab heavy chain (chains B)
QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKY
SGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVTVS

Sequence of entity 3 (C), FASTA

>9PNS_3 15B8 Fab light chain (chains C)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGS
GVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEIK

Ligands and cofactors

ID	Name	Formula	Copies
A1CIZ	(6M)-1-methyl-6-(1,2,5,6-tetrahydropyridin-3-yl)-1H-indole	C14 H16 N2	1

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

Primary citation

Large Library Docking for Polypharmacology. Wu, Y., Vigneron, S., Braz, J. et al. J Med Chem (2026) 69:6210-6229. DOI 10.1021/acs.jmedchem.5c03810 · 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…
5I71 3.15 Å, X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram at…
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…
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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