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9qf1

Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 2

Method: X-RAY DIFFRACTION D_max: 62.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qf1
deposition_date	2025-03-11
last_revision	2025-08-27
title	Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 2
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	16.04 Å
rg_electron	15.28 Å
i0	8399010.00
molecular_weight	14083.0 kDa
excluded_volume	13469 Å³
envelope_volume	21025 Å³
shell_volume	12120 Å³
envelope_diameter	61.2 Å
shell_rg	20.49 Å
envelope_rg	15.77 Å
shape_rg	15.29 Å
total_rg	16.02 Å
total_atoms	1062
n_residues	131
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	62.4 Å
rg_real	16.05 Å
rg_real_error	0.54 Å
i0_real	8.3990e+06
i0_real_error	1.0150e+05
rg_reciprocal	16.05 Å
i0_reciprocal	8399000.0000
total_estimate	0.7936
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	18.9 Å
skewness	0.423
kurtosis	-0.002
angular_range	— – 0.4950 Å⁻¹
current_alpha	0.0000
highest_alpha	2511000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.545; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.678; Smooth: 0.999

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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	1125

GSHMSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAKKKRWNSIEERR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;~{N}-methyl-~{N}-[(1~{R})-1-pyridin-2-yl-3-pyrrolidin-1-yl-propyl]-5-[4,5,6,7-tetrakis(fluoranyl)-1~{H}-indol-3-yl]-1,3,4-oxadiazol-2-amine ;
formula_weight	474.5 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	63

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6. Citations (1)

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length_a	47.108 Å
length_b	71.264 Å
length_c	75.945 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	1.511 Å
resolution_low	37.970 Å
r_factor	0.1967
r_work	0.1955
r_free	0.2186

fit	/app/data/saxs_computation/qf/9qf1/9qf1.fit
pddf	/app/data/pr_computation/qf/9qf1/9qf1.pr.out
profile	/app/data/saxs_computation/qf/9qf1/9qf1.dat

Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 2

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