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9qdz

GID4 in complex with Compound 14

Method: X-RAY DIFFRACTION D_max: 58.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdz
deposition_date	2025-03-07
last_revision	2026-03-18
title	GID4 in complex with Compound 14
keywords	E3 Ubiquitin ligase, ubiquitination, Targeted Protein Degradation, 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	16.71 Å
rg_electron	15.69 Å
i0	12358000.00
molecular_weight	18180.0 kDa
excluded_volume	17902 Å³
envelope_volume	27563 Å³
shell_volume	14814 Å³
envelope_diameter	58.0 Å
shell_rg	21.58 Å
envelope_rg	16.11 Å
shape_rg	15.66 Å
total_rg	16.55 Å
total_atoms	1386
n_residues	161
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	58.6 Å
rg_real	16.65 Å
rg_real_error	0.39 Å
i0_real	1.2360e+07
i0_real_error	1.4810e+05
rg_reciprocal	16.65 Å
i0_reciprocal	12360000.0000
total_estimate	0.8471
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.6 Å
skewness	0.303
kurtosis	-0.124
angular_range	— – 0.4750 Å⁻¹
current_alpha	0.0000
highest_alpha	2783000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.674; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	1434

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-(5-methyl-4-piperidin-1-ylcarbonyl-furan-2-yl)phenyl]-4,4-dimethyl-piperidine-1-carboximidamide
formula_weight	440.6 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	48

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6. Citations (1)

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length_a	38.090 Å
length_b	40.390 Å
length_c	52.870 Å
angle_alpha	90.00 °
angle_beta	108.69 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	31.440 Å
r_factor	0.1840
r_work	0.1808
r_free	0.2436

fit	/app/data/saxs_computation/qd/9qdz/9qdz.fit
pddf	/app/data/pr_computation/qd/9qdz/9qdz.pr.out
profile	/app/data/saxs_computation/qd/9qdz/9qdz.dat

GID4 in complex with Compound 14

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