SAXSdb — 9wjh

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1. Structure Basics

entry_id	9wjh
deposition_date	2025-08-31
title	Spiroindoline-bound human VAChT
keywords	VAChT, SLC18A3, Acetylcholine, Spiroindoline, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	21.90 Å
rg_electron	21.01 Å
i0	52702200.00
molecular_weight	39600.0 kDa
excluded_volume	39320 Å³
envelope_volume	65839 Å³
shell_volume	25403 Å³
envelope_diameter	75.4 Å
shell_rg	28.44 Å
envelope_rg	21.51 Å
shape_rg	21.02 Å
total_rg	21.71 Å
total_atoms	3010
n_residues	393
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	73.8 Å
rg_real	22.37 Å
rg_real_error	0.18 Å
i0_real	5.2160e+07
i0_real_error	6.0190e+05
rg_reciprocal	21.82 Å
i0_reciprocal	52700000.0000
total_estimate	0.6771
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	26.4 Å
skewness	0.399
kurtosis	-0.019
angular_range	— – 0.3650 Å⁻¹
current_alpha	5.7080
highest_alpha	10140000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 0.922; Sysdev: 0.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.597

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Maltose/maltodextrin-binding periplasmic protein,Vesicular acetylcholine transporter,DARPins
formula_weight	112705.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3013

MEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLIDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQAEEEKRKAEEEKRKLVLVIVCVALLLDNMLYMVIVPIVPDYIAHMRGGGEGPTRTPEVWEPTLPLPTPANASAYTANTSASPTAAWPAGSALRPRYPTESEDVKIGVLFASKAILQLLVNPLSGPFIDRMSYDVPLLIGLGVMFASTVLFAFAEDYATLFAARSLQGLGSAFADTSGIAMIADKYPEEPERSRALGVALAFISFGSLVAPPFGGILYEFAGKRVPFLVLAAVSLFDALLLLAVAKPFSAAARARANLPVGTPIHRLMLDPYIAVVAGALTTCNIPLAFLEPTIATWMKHTMAASEWEMGMAWLPAFVPHVLGVYLTVRLAARYPHLQWLYGALGLAVIGASSCIVPACRSFAPLVVSLCGLCFGIALVDTALLPTLAFLVDVRHVSVYGSVYAIADISYSVAYALGPIVAGHIVHSLGFEQLSLGMGLANLLYAPVLLLLRNVGLLTRSRSERDVLLDEPPQGLYDAVRLRERPVSGQDGEPRSPPGPFDECEDDGGGGSGGGGSDLGRKLLEAARAGQLDEVRILLANGADVNAADNTGTTPLHLAAYSGHLEIVEVLLKHGADVDASDVFGYTPLHLAAYWGHLEIVEVLLKNGADVNAMDSDGMTPLHLAAKWGYLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLNLEGGSLEVLFQ

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Homo sapiens

Entity 2 non-polymer

description	(6-bromanylpyridin-3-yl)-[1'-[(~{E})-3-(4-chlorophenyl)prop-2-enyl]-5-fluoranyl-spiro[2~{H}-indole-3,4'-piperidine]-1-yl]methanone
formula_weight	540.9 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.40 Å
resolution_method	—
num_particles	328769

fit	/app/data/saxs_computation/wj/9wjh/9wjh.fit
pddf	/app/data/pr_computation/wj/9wjh/9wjh.pr.out
profile	/app/data/saxs_computation/wj/9wjh/9wjh.dat

Spiroindoline-bound human VAChT

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D