Outward-open structure of human serotonin transporter bound to vilazodone. Determined by electron microscopy at 2.78 Å resolution. Released 17 Sept 2025.
Explore 9HCO in 3D Show helices and sheets RCSB PDB PDBe
9HCO contains 45 α-helices and 33 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 85-96 | 12 | |
| α-helix | 99-111 | 13 | |
| α-helix | 118-124 | 7 | |
| α-helix | 125-129 | 5 | |
| α-helix | 130-143 | 14 | |
| α-helix | 149-153 | 5 | |
| α-helix | 156-158 | 3 | |
| α-helix | 160-189 | 30 | |
| 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 | |
| α-helix | 245-247 | 3 | |
| β-strand | 251 | 1 | 2 |
| α-helix | 253-270 | 18 | |
| α-helix | 274-284 | 11 | |
| α-helix | 287-301 | 15 | |
| α-helix | 305-313 | 9 | |
| α-helix | 318-321 | 4 | |
| α-helix | 323-337 | 15 | |
| α-helix | 343-348 | 6 | |
| α-helix | 357-390 | 34 | |
| α-helix | 394-396 | 3 | |
| α-helix | 404 | 1 | |
| α-helix | 405-409 | 5 | |
| α-helix | 410-416 | 7 | |
| α-helix | 423-453 | 31 | |
| α-helix | 466-478 | 13 | |
| α-helix | 479-481 | 3 | |
| β-strand | 482 | 1 | 2 |
| α-helix | 485-494 | 10 | |
| α-helix | 499-510 | 12 | |
| 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 | 560-561 | 2 | |
| β-strand | 564 | 1 | 3 |
| β-strand | 569 | 1 | 3 |
| α-helix | 570-571 | 2 | |
| α-helix | 572-586 | 15 | |
| α-helix | 589-599 | 11 | |
| α-helix | 604-612 | 9 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 22-25 | 4 | 4 |
| β-strand | 29 | 1 | 5 |
| β-strand | 36-44 | 9 | 4 |
| α-helix | 48-50 | 3 | |
| β-strand | 53-58 | 6 | 6 |
| β-strand | 64-68 | 5 | 6 |
| β-strand | 71 | 1 | 7 |
| β-strand | 76 | 1 | 7 |
| β-strand | 79 | 1 | 6 |
| β-strand | 87-92 | 6 | 4 |
| β-strand | 97-103 | 7 | 4 |
| α-helix | 107-109 | 3 | |
| β-strand | 112-117 | 6 | 6 |
| α-helix | 121-123 | 3 | |
| β-strand | 129-130 | 2 | 6 |
| β-strand | 134-135 | 2 | 6 |
| β-strand | 136 | 1 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 24-25 | 2 | 8 |
| β-strand | 30-32 | 3 | 9 |
| α-helix | 33-34 | 2 | |
| β-strand | 39-45 | 7 | 8 |
| β-strand | 50-51 | 2 | 10 |
| β-strand | 54-55 | 2 | 10 |
| β-strand | 57-62 | 6 | 9 |
| β-strand | 69-73 | 5 | 9 |
| β-strand | 77-78 | 2 | 9 |
| β-strand | 86-91 | 6 | 8 |
| β-strand | 94-99 | 6 | 8 |
| α-helix | 104-106 | 3 | |
| β-strand | 109-114 | 6 | 9 |
| β-strand | 121 | 1 | 9 |
| β-strand | 126-129 | 4 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Sodium-dependent serotonin transporter | A | protein | 685 | Homo sapiens | P31645 (AlphaFold model) |
| 15B8 Fab heavy chain | H | protein | 229 | Mus musculus | |
| 15B8 Fab light chain | L | protein | 216 | Mus musculus |
>9HCO_1 Sodium-dependent serotonin transporter (chains A) METTPLNSQKQLSACEDGEDCQENGVLQKVVPTPGDKVESGQISNGYSAVPSPGAGDDTR HSIPATTTTLVAELHQGERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLP YTIMAIFGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIM AWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIH RSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGA TLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQD ALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPAS TFFAIIFFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVT LTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRIC WVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIIT PGTFKERIIKSITPETPTEIPCGDIRLNAVGGSLVPRGSGGSWSHPQFEKGGGSGGGSGG SAWSHPQFEKGGSHHHHHHHHHHHH
>9HCO_2 15B8 Fab heavy chain (chains H) QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKY SGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVTVS SAKTTAPSVFPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQS GLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKLVPRGSHHHHHH
>9HCO_3 15B8 Fab light chain (chains L) DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGS GVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEIKRADAAPTVS VFPPSSEQLTSGGASVVCFLNNFYPRDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRG
| ID | Name | Formula | Copies |
|---|---|---|---|
| YG7 | 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide | C26 H27 N5 O2 | 1 |
Water and common crystallization additives (CL, NA) are not listed.
Structural basis of vilazodone dual binding mode to the serotonin transporter. Kalenderoglou, I.E., Nygaard, A., Vogt, C.D. et al. Nat Commun (2025) 16:10119-10119. DOI 10.1038/s41467-025-65202-3 · PubMed
Other PDB entries of the same protein (UniProt P31645 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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