SAXSdb — 9w4t

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1. Structure Basics

entry_id	9w4t
deposition_date	2025-08-01
title	ratTRPV1 bound with antagonist AMG9810
keywords	antagonist, complex, 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	44.20 Å
rg_electron	43.33 Å
i0	776842000.00
molecular_weight	248240.0 kDa
excluded_volume	317560 Å³
envelope_volume	437800 Å³
shell_volume	80811 Å³
envelope_diameter	135.9 Å
shell_rg	51.60 Å
envelope_rg	42.16 Å
shape_rg	43.32 Å
total_rg	43.73 Å
total_atoms	35089
n_residues	2148
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	132.6 Å
rg_real	43.84 Å
rg_real_error	0.94 Å
i0_real	7.7680e+08
i0_real_error	1.4640e+07
rg_reciprocal	44.19 Å
i0_reciprocal	777200000.0000
total_estimate	0.8901
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	62.6 Å
skewness	-0.044
kurtosis	-0.525
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	49190000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.875

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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,Transient receptor potential cation channel subfamily V member 1
formula_weight	140466.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	35089

MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSGTGGGSGDDDDKSPMGSHHHHHHHHGSDYDIPTTENLYFQGAMDPMEQRASLDSEESESPPQENSCLDPPDRDPNCKPPPVKPHIFTTRSRTRLFGKGDSEEASPLDCPYEEGGLASCPIITVSSVLTIQRPGDGPASVRPSSQDSVSAGEKPPRLYDRRSIFDAVAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNLHNGQNDTIALLLDVARKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGADVQAAANGDFFKKTKGRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGNTVLHALVEVADNTVDNTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGKIGVLAYILQREIHEPECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKNNSLPMESTPHKCRGSACKPGNSYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLLQVGFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPGNCEGVKRTLSFSLRSGRVSGRNWKNFALVPLLRDASTRDRHATQQEEVQLKHYTGSLKPEDAEVFKDSMVPGEK

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Homo sapiens

Entity 2 non-polymer

description	(~{Z})-3-(4-~{tert}-butylphenyl)-~{N}-(2,3-dihydro-1,4-benzodioxin-6-yl)prop-2-enamide
formula_weight	337.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

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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	2.87 Å
resolution_method	—
num_particles	115503

fit	/app/data/saxs_computation/w4/9w4t/9w4t.fit
pddf	/app/data/pr_computation/w4/9w4t/9w4t.pr.out
profile	/app/data/saxs_computation/w4/9w4t/9w4t.dat

ratTRPV1 bound with antagonist AMG9810

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