SAXSdb — 9vu9

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1. Structure Basics

entry_id	9vu9
deposition_date	2025-07-12
title	channel D complex with 4
keywords	channel D complex with 4, MEMBRANE PROTEIN; MEMBRANE 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	41.96 Å
rg_electron	41.23 Å
i0	798223000.00
molecular_weight	156140.0 kDa
excluded_volume	152440 Å³
envelope_volume	333820 Å³
shell_volume	67197 Å³
envelope_diameter	140.3 Å
shell_rg	47.13 Å
envelope_rg	40.19 Å
shape_rg	41.24 Å
total_rg	41.47 Å
total_atoms	11841
n_residues	1551
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	130.1 Å
rg_real	41.74 Å
rg_real_error	0.95 Å
i0_real	7.9820e+08
i0_real_error	1.4480e+07
rg_reciprocal	41.96 Å
i0_reciprocal	798400000.0000
total_estimate	0.8930
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.8 Å
skewness	0.088
kurtosis	-0.474
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	36730000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.924

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Calmodulin-1
formula_weight	16852.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	E,F,G
atom_count	11841

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Small conductance calcium-activated potassium channel protein 2
formula_weight	63841.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D

MSSCRYNGGVMRPLSNLSASRRNLHEMDSEAQPLQPPASVGGGGGASSPSAAAAAAAAVSSSAPEIVVSKPEHNNSNNLALYGTGGGGSTGGGGGGGGSGHGSSSGTKSSKKKNQNIGYKLGHRRALFEKRKRLSDYALIFGMFGIVVMVIETELSWGAYDKASLYSLALKCLISLSTIILLGLIIVYHAREIQLFMVDNGADDWRIAMTYERIFFICLEILVCAIHPIPGNYTFTWTARLAFSYAPSTTTADVDIILSIPMFLRLYLIARVMLLHSKLFTDASSRSIGALNKINFNTRFVMKTLMTICPGTVLLVFSISLWIIAAWTVRACERYHDQQDVTSNFLGAMWLISITFLSIGYGDMVPNTYCGKGVCLLTGIMGAGCTALVVAVVARKLELTKAEKHVHNFMMDTQLTKRVKNAAANVLRETWLIYKNTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQNIMYDMISDLNERSEDFEKRIVTLETKLETLIGSIHALPGLISQTIRQQQRDFIEAQMESYDKHVTYNAERSRSSSRRRRSSSTAPPTSSESS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 non-polymer

description	(3~{S})-3-(1~{H}-benzimidazol-2-ylamino)-~{N}-(cyanomethyl)-~{N}-methyl-3-[3-(trifluoromethyl)phenyl]propanamide
formula_weight	401.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	4

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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	3.340 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.34 Å
resolution_method	—
num_particles	62486

fit	/app/data/saxs_computation/vu/9vu9/9vu9.fit
pddf	/app/data/pr_computation/vu/9vu9/9vu9.pr.out
profile	/app/data/saxs_computation/vu/9vu9/9vu9.dat

channel D complex with 4

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

Refinement

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)