SAXSdb — 9yj4

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1. Structure Basics

entry_id	9yj4
deposition_date	2025-10-03
last_revision	2026-05-20
title	TGM6-D3 bound to mouse TBRII
keywords	Inhibitor, Complex, TGF-beta, Parasite, Molecular Mimicry, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

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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	24.19 Å
rg_electron	23.60 Å
i0	34918300.00
molecular_weight	43378.0 kDa
excluded_volume	53321 Å³
envelope_volume	68062 Å³
shell_volume	24482 Å³
envelope_diameter	85.3 Å
shell_rg	30.09 Å
envelope_rg	23.86 Å
shape_rg	23.64 Å
total_rg	24.27 Å
total_atoms	3013
n_residues	378
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	81.9 Å
rg_real	24.11 Å
rg_real_error	0.46 Å
i0_real	3.4920e+07
i0_real_error	4.3410e+05
rg_reciprocal	24.13 Å
i0_reciprocal	34920000.0000
total_estimate	0.8852
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.4 Å
skewness	0.199
kurtosis	-0.441
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	5459000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Transforming growth factor beta mimic 6
formula_weight	10098.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	3150

TGSSCPPLPDDETVWYEYYGYVDGRHTVGDAAIKDSLENYPPNTHARRHCKALSKKADPGEFVAICYQRRGTSESQWQYYPRIASCPDP

Source

organism	Heligmosomoides polygyrus
ncbi_taxonomy_id	6339
host_organism	Homo sapiens

Entity 2 polymer

description	TGF-beta receptor type-2
formula_weight	11999.0 kDa
ec_number	2.7.11.30
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

KLPQLCKFCDVRLSTCDNQKSCMSNCSITAICEKPHEVCVAVWRKNDKNITLETVCHDPKLTYHGFTLEDAASPKCVMKEKKRAGETFFMCACNMEECNDYIIFS

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	137

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6. Citations (1)

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length_a	53.353 Å
length_b	92.589 Å
length_c	93.393 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.520 Å
resolution_low	32.880 Å
r_factor	0.2599
r_work	0.2585
r_free	0.2880

fit	/app/data/saxs_computation/yj/9yj4/9yj4.fit
pddf	/app/data/pr_computation/yj/9yj4/9yj4.pr.out
profile	/app/data/saxs_computation/yj/9yj4/9yj4.dat

TGM6-D3 bound to mouse TBRII

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

Diffraction

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)