GID4 in complex with Compound 9

Method: X-RAY DIFFRACTION D_max: 58.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdy
deposition_date	2025-03-07
last_revision	2026-03-18
title	GID4 in complex with Compound 9
keywords	Ligase, Ubiquitination, TPD; 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	16.63 Å
rg_electron	15.51 Å
i0	11747600.00
molecular_weight	17598.0 kDa
excluded_volume	17287 Å³
envelope_volume	27009 Å³
shell_volume	14609 Å³
envelope_diameter	59.9 Å
shell_rg	21.53 Å
envelope_rg	16.06 Å
shape_rg	15.46 Å
total_rg	16.42 Å
total_atoms	1341
n_residues	158
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	58.7 Å
rg_real	16.56 Å
rg_real_error	0.35 Å
i0_real	1.1750e+07
i0_real_error	1.2810e+05
rg_reciprocal	16.56 Å
i0_reciprocal	11750000.0000
total_estimate	0.7670
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.6 Å
skewness	0.303
kurtosis	-0.098
angular_range	— – 0.4800 Å⁻¹
current_alpha	0.0000
highest_alpha	2663000.0000
n_real_points	78
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.657; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (1)

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length_a	38.065 Å
length_b	40.274 Å
length_c	54.394 Å
angle_alpha	90.00 °
angle_beta	110.38 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	35.670 Å
r_factor	0.2147
r_work	0.2127
r_free	0.2541

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

type	polypeptide(L)
strand_id	A
atom_count	1356

GID4 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

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

description	~{N}-[3-fluoranyl-5-(5-methylfuran-2-yl)phenyl]-4-methyl-piperidine-1-carboximidamide
formula_weight	315.4 kDa
src_method	syn
entity_count	1

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	15

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