6AWN: S439T human serotonin transporter

X-ray structure of the S439T human serotonin transporter complexed with paroxetine at the central site. Determined by X-ray diffraction at 3.62 Å resolution. Released 25 Oct 2017.

Method: X-ray diffraction
Resolution: 3.62 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 7,703
Mol. weight: 112 kDa
Ligands: 8PR, LMT, CLR, NAG
Released: 25 Oct 2017

Explore 6AWN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AWN contains 52 α-helices and 54 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	79-80	2
α-helix	85-96	12
α-helix	99-111	13
α-helix	114-117	4
α-helix	118-123	6
α-helix	124-129	6
α-helix	130-143	14
α-helix	149-152	4
α-helix	156-159	4
α-helix	160-188	29
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	253-270	18
α-helix	274-284	11
α-helix	287-300	14
α-helix	306-313	8
α-helix	317-321	5
α-helix	323-337	15
α-helix	343-349	7
α-helix	358-389	32
α-helix	396-398	3
α-helix	403-404	2
α-helix	405-409	5
α-helix	410-415	6
α-helix	420-453	34
β-strand	455	1	3
β-strand	458	1	3
α-helix	462-477	16
β-strand	482	1	2
α-helix	485-491	7
α-helix	492-496	5
α-helix	497-510	14
α-helix	511-515	5
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	560-562	3
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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	5
β-strand	29-31	3	6
β-strand	37-39	3	5
β-strand	41-44	4	5
α-helix	48-50	3
β-strand	52-58	7	7
β-strand	64-70	7	7
β-strand	78-79	2	7
β-strand	84	1	5
β-strand	87-92	6	5
β-strand	97-102	6	5
β-strand	112-118	7	7
β-strand	128	1	7
β-strand	132-133	2	7
β-strand	134-136	3	6
β-strand	142	1	8
α-helix	143-144	2
β-strand	145-149	5	9
β-strand	160-170	11	9
β-strand	171	1	8
β-strand	176-179	4	10
β-strand	188-196	9	9
β-strand	199-209	11	9
α-helix	210-212	3
β-strand	219-224	6	10
β-strand	229-234	6	10

Chain C: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	11
β-strand	30-34	5	12
β-strand	39-44	6	11
β-strand	50	1	13
β-strand	53-58	6	12
β-strand	65-69	5	12
β-strand	73-74	2	12
α-helix	75	1
β-strand	82-85	4	11
β-strand	88	1	13
β-strand	90-95	6	11
α-helix	100-102	3
β-strand	105-110	6	12
α-helix	116	1
β-strand	118	1	12
β-strand	122-127	6	12
β-strand	131	1	14
β-strand	134-138	5	15
α-helix	139-141	3
α-helix	142-147	6
β-strand	149-159	11	15
β-strand	160	1	14
β-strand	165-169	5	16
β-strand	174-175	2	16
β-strand	179-183	5	15
α-helix	184-187	4
β-strand	193-202	10	15
α-helix	203-206	4
β-strand	212-217	6	16
α-helix	224	1
β-strand	225-229	5	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium-dependent serotonin transporter	A	protein	549	Homo sapiens	P31645 (AlphaFold model)
8B6 antibody FAB heavy chain	B	protein	229	Mus musculus	A0A0F7R1P3 (AlphaFold model)
8B6 antibody FAB light chain	C	protein	214	Mus musculus	A0A0F7R5U8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6AWN_1 Sodium-dependent serotonin transporter (chains A)
GSQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICAQNGGGAFLLPYTIMAIFGGIPLF
YMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTD
QLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISW
QLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIALSVLLVRGATLPGAWRGVLFYL
KPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSF
VSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLIT
LGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLE
EYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFII
ASFLMSPPQLRLFQYNYPYWSIILGYAIGTSSFICIPTYIAYRLIITPGTFKERIIKSIT
PETPTLVPR

Sequence of entity 2 (B), FASTA

>6AWN_2 8B6 antibody FAB heavy chain (chains B)
EVQLQQSGPELVKPGASVKISCKASGYTFTDYYMNWVKQSHGKSLEWIGNINPNNGGTSY
NQKFKGKATLTVDKSSTTAYMELRSLTSEDSAVYYCTRSPVRPYYFDYWGQGTTLTVSSA
KTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGL
YTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPRGSHHHHHHHH

Sequence of entity 3 (C), FASTA

>6AWN_3 8B6 antibody FAB light chain (chains C)
DIVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKPGQSPKLLIYSASYRYTGVPD
RFTGSGSGTDFTFTISSVQAEDLAVYYCQQHYSIPRTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
8PR	Paroxetine	C19 H20 F N O3	1
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	1
CLR	Cholesterol	C27 H46 O	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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

Primary citation

Structural basis for recognition of diverse antidepressants by the human serotonin transporter. Coleman, J.A., Gouaux, E. Nat Struct Mol Biol (2018) 25:170-175. DOI 10.1038/s41594-018-0026-8 · 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…
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…

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