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9qfy

Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 9.

Method: X-RAY DIFFRACTION D_max: 60.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qfy
deposition_date	2025-03-12
last_revision	2025-08-27
title	Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 9.
keywords	E3 ubiquitin ligase, LIGASE; LIGASE
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	15.75 Å
rg_electron	14.98 Å
i0	7867590.00
molecular_weight	13621.0 kDa
excluded_volume	13024 Å³
envelope_volume	20077 Å³
shell_volume	11824 Å³
envelope_diameter	60.1 Å
shell_rg	20.20 Å
envelope_rg	15.40 Å
shape_rg	14.97 Å
total_rg	15.74 Å
total_atoms	1025
n_residues	128
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	60.0 Å
rg_real	15.76 Å
rg_real_error	0.57 Å
i0_real	7.8680e+06
i0_real_error	1.0540e+05
rg_reciprocal	15.76 Å
i0_reciprocal	7868000.0000
total_estimate	0.8083
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.5 Å
skewness	0.408
kurtosis	-0.057
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	2383000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.591; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.732; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	E3 ubiquitin-protein ligase CHIP
formula_weight	15635.8 kDa
ec_number	2.3.2.27
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1205

GSHMSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAKKKRWNSIEERR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	~{N},~{N}-dimethyl-1-[(3~{S})-1-[[4,5,6,7-tetrakis(fluoranyl)-1~{H}-indol-3-yl]carbonyl]piperidin-3-yl]methanesulfonamide
formula_weight	421.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	165

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6. Citations (1)

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length_a	47.067 Å
length_b	72.570 Å
length_c	76.925 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.064 Å
resolution_low	39.490 Å
r_factor	0.1962
r_work	0.1957
r_free	0.2058

fit	/app/data/saxs_computation/qf/9qfy/9qfy.fit
pddf	/app/data/pr_computation/qf/9qfy/9qfy.pr.out
profile	/app/data/saxs_computation/qf/9qfy/9qfy.dat

Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 9.

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