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9qzi

GID4 in complex with Compound 21

Method: X-RAY DIFFRACTION D_max: 57.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qzi
deposition_date	2025-04-23
last_revision	2026-05-06
title	GID4 in complex with Compound 21
keywords	Ligase, TPD, GID4, Compound, Complex, Targeted Protein Degradation, Ubiquitination; 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	16.69 Å
rg_electron	15.66 Å
i0	12049900.00
molecular_weight	17962.0 kDa
excluded_volume	17716 Å³
envelope_volume	27623 Å³
shell_volume	14810 Å³
envelope_diameter	56.2 Å
shell_rg	21.76 Å
envelope_rg	16.15 Å
shape_rg	15.62 Å
total_rg	16.56 Å
total_atoms	1370
n_residues	159
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	57.5 Å
rg_real	16.63 Å
rg_real_error	0.31 Å
i0_real	1.2050e+07
i0_real_error	1.4470e+05
rg_reciprocal	16.64 Å
i0_reciprocal	12050000.0000
total_estimate	0.7162
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	20.2 Å
skewness	0.304
kurtosis	-0.122
angular_range	— – 0.4750 Å⁻¹
current_alpha	0.0000
highest_alpha	2765000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 0.394; Positv: 1.000; Valcen: 0.998; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Glucose-induced degradation protein 4 homolog
formula_weight	19547.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1379

SGSKFRGHQKSKGNSYDVEVVLQHVDTGNSYLCGYLKIKGLTEEYPTLTTFFEGEIISKKHPFLTRKWDADEDVDRKHWGKFLAFYQYAKSFNSDDFDYEELKNGDYVFMRWKEQFLVPDHTIKDISGASFAGFYYICFQKSAASIEGYYYHRSSEWYQSLNLTHV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;~{N}-[3-fluoranyl-5-[4-[(3~{S})-3-[2-(2-methoxyethoxy)ethyl]piperidin-1-yl]carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide ;
formula_weight	542.7 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	9

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6. Citations (1)

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length_a	40.273 Å
length_b	41.930 Å
length_c	103.135 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.000 Å
resolution_low	37.540 Å
r_factor	0.2215
r_work	0.2199
r_free	0.2530

fit	/app/data/saxs_computation/qz/9qzi/9qzi.fit
pddf	/app/data/pr_computation/qz/9qzi/9qzi.pr.out
profile	/app/data/saxs_computation/qz/9qzi/9qzi.dat

GID4 in complex with Compound 21

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