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9qzg

GID4 in complex with Compound 18

Method: X-RAY DIFFRACTION D_max: 58.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qzg
deposition_date	2025-04-23
last_revision	2026-05-06
title	GID4 in complex with Compound 18
keywords	Ligase, TPD, 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	16.71 Å
rg_electron	15.69 Å
i0	12029600.00
molecular_weight	17954.0 kDa
excluded_volume	17692 Å³
envelope_volume	27529 Å³
shell_volume	14770 Å³
envelope_diameter	58.2 Å
shell_rg	21.68 Å
envelope_rg	16.17 Å
shape_rg	15.65 Å
total_rg	16.56 Å
total_atoms	1369
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	58.1 Å
rg_real	16.65 Å
rg_real_error	0.27 Å
i0_real	1.2030e+07
i0_real_error	1.3270e+05
rg_reciprocal	16.66 Å
i0_reciprocal	12030000.0000
total_estimate	0.8536
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.4 Å
skewness	0.305
kurtosis	-0.135
angular_range	— – 0.4750 Å⁻¹
current_alpha	0.0000
highest_alpha	2789000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.992

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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	1380

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-(4-methoxypiperidin-1-yl)carbonyl-5-methyl-furan-2-yl]phenyl]-4,4-dimethyl-piperidine-1-carboximidamide
formula_weight	470.6 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	11

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6. Citations (1)

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length_a	40.255 Å
length_b	41.752 Å
length_c	103.205 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	1.900 Å
resolution_low	38.730 Å
r_factor	0.2787
r_work	0.2757
r_free	0.3358

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

GID4 in complex with Compound 18

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