Crystal structure of STUB1 complexed with a compound molecule

Method: X-RAY DIFFRACTION D_max: 50.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r1p
deposition_date	2025-04-28
last_revision	2025-09-17
title	Crystal structure of STUB1 complexed with a compound molecule
keywords	STIP1 homology and U-Box containing protein 1, E3 ubiquitin ligase, CELL CYCLE; CELL CYCLE
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	15.70 Å
rg_electron	14.51 Å
i0	4383680.00
molecular_weight	14492.0 kDa
excluded_volume	17990 Å³
envelope_volume	20432 Å³
shell_volume	12067 Å³
envelope_diameter	51.4 Å
shell_rg	20.05 Å
envelope_rg	14.86 Å
shape_rg	14.58 Å
total_rg	15.45 Å
total_atoms	2016
n_residues	123
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	50.6 Å
rg_real	15.61 Å
rg_real_error	0.32 Å
i0_real	4.3840e+06
i0_real_error	4.8480e+04
rg_reciprocal	15.62 Å
i0_reciprocal	4384000.0000
total_estimate	0.8180
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	20.5 Å
skewness	0.127
kurtosis	-0.448
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	936600.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (1)

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length_a	89.948 Å
length_b	89.948 Å
length_c	53.597 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	2.290 Å
resolution_low	44.970 Å
r_factor	0.2067
r_work	0.2052
r_free	0.2339

description	E3 ubiquitin-protein ligase CHIP
formula_weight	15792.9 kDa
ec_number	2.3.2.27
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2022

Crystal structure of STUB1 complexed with a compound molecule

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

description	1-[3-[1-methyl-4-(pyridin-3-ylmethylamino)pyrazolo[3,4-d]pyrimidin-6-yl]phenyl]-3-[3-(trifluoromethyl)phenyl]thiourea
formula_weight	534.6 kDa
src_method	syn
entity_count	1

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

fit	/app/data/saxs_computation/r1/9r1p/9r1p.fit
pddf	/app/data/pr_computation/r1/9r1p/9r1p.pr.out
profile	/app/data/saxs_computation/r1/9r1p/9r1p.dat