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9pns

Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc and NaCl

Method: ELECTRON MICROSCOPY D_max: 110.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pns
deposition_date	2025-07-21
title	Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc and NaCl
keywords	Neurotransmitter Transporter, Inhibitor, Complex, TRANSPORT PROTEIN-IMMUNE SYSTEM-INHIBITOR complex; TRANSPORT PROTEIN/IMMUNE SYSTEM/INHIBITOR
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	32.31 Å
rg_electron	32.04 Å
i0	202084000.00
molecular_weight	79535.0 kDa
excluded_volume	78766 Å³
envelope_volume	132970 Å³
shell_volume	36313 Å³
envelope_diameter	118.7 Å
shell_rg	37.16 Å
envelope_rg	32.41 Å
shape_rg	32.02 Å
total_rg	32.40 Å
total_atoms	6049
n_residues	765
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	110.8 Å
rg_real	32.62 Å
rg_real_error	0.92 Å
i0_real	2.0210e+08
i0_real_error	3.1210e+06
rg_reciprocal	32.50 Å
i0_reciprocal	202100000.0000
total_estimate	0.8317
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.6 Å
skewness	0.539
kurtosis	-0.331
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	28080000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.832; Smooth: 0.795

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Sodium-dependent serotonin transporter
formula_weight	61062.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6049

GERETWGKKVDFLLSVIGYAVDLGNVWRFPYICYQNGGGAFLLPYTIMAIFGGIPLFYMELALGQYHRNGCISIWRKICPIFKGIGYAICIIAFYIASYYNTIMAWALYYLISSFTDQLPWTSCKNSWNTGNCTNYFSEDNITWTLHSTSPAEEFYTRHVLQIHRSKGLQDLGGISWQLALCIMLIFTVIYFSIWKGVKTSGKVVWVTATFPYIILSVLLVRGATLPGAWRGVLFYLKPNWQKLLETGVWIDAAAQIFFSLGPGFGVLLAFASYNKFNNNCYQDALVTSVVNCMTSFVSGFVIFTVLGYMAEMRNEDVSEVAKDAGPSLLFITYAEAIANMPASTFFAIIFFLMLITLGLDSTFAGLEGVITAVLDEFPHVWAKRRERFVLAVVITCFFGSLVTLTFGGAYVVKLLEEYATGPAVLTVALIEAVAVSWFYGITQFCRDVKEMLGFSPGWFWRICWVAISPLFLLFIICSFLMSPPQLRLFQYNYPYWSIILGYCIGTSSFICIPTYIAYRLIITPGTFKERIIKSITPETP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	15B8 Fab heavy chain
formula_weight	13166.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVQLQQSGPELVKLGASVRISCKASGYRFSYSWMNWVKQRPGKGLEWIGRIYPGDGDTKYSGKFKGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARSAYGSEGFAMDYWGQGTSVTVS

Source

organism	Mus musculus
common_name	mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	15B8 Fab light chain
formula_weight	11905.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFLNWFQQKPGQPPKLLIYAASNQGSGVPARFSGSGSGTYFSLNIHPMEEDDTAVYFCQQTKGVSWTFGGGTKVEIK

Source

organism	Mus musculus
common_name	mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	(6M)-1-methyl-6-(1,2,5,6-tetrahydropyridin-3-yl)-1H-indole
formula_weight	212.3 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	3.40 Å
resolution_method	—
num_particles	9815

fit	/app/data/saxs_computation/pn/9pns/9pns.fit
pddf	/app/data/pr_computation/pn/9pns/9pns.pr.out
profile	/app/data/saxs_computation/pn/9pns/9pns.dat

Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc and NaCl

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)