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9y8s

Crystal structure of the Kelch domain of human KLHL12 with compound 9k

Method: X-RAY DIFFRACTION D_max: 55.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y8s
deposition_date	2025-09-11
title	Crystal structure of the Kelch domain of human KLHL12 with compound 9k
keywords	E3 ligase, fragment-based drug discovery, PROTAC, 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	18.78 Å
rg_electron	17.51 Å
i0	17936700.00
molecular_weight	31586.0 kDa
excluded_volume	39181 Å³
envelope_volume	43332 Å³
shell_volume	19956 Å³
envelope_diameter	56.2 Å
shell_rg	24.52 Å
envelope_rg	17.70 Å
shape_rg	17.46 Å
total_rg	18.60 Å
total_atoms	4354
n_residues	287
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	55.9 Å
rg_real	18.61 Å
rg_real_error	0.23 Å
i0_real	1.7940e+07
i0_real_error	1.8350e+05
rg_reciprocal	18.64 Å
i0_reciprocal	17940000.0000
total_estimate	0.9024
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.3 Å
skewness	0.013
kurtosis	-0.551
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	7074000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Kelch-like protein 12
formula_weight	32148.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4756

GSHMGSANEVLLVVGGFGSQQSPIDVVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGGYDGRSRLSSVECLDYTADEDGVWYSVAPMNVRRGLAGATTLGDMIYVSGGFDGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIYCLGGYDGLNILNSVEKYDPHTGHWTNVTPMATKRSGAGVALLNDHIYVVGGFDGTAHLSSVEAYNIRTDSWTTVTSMTTPRCYVGATVLRGRLYAIAGYDGNSLLSSIECYDPIIDSWEVVTSMGTQRCDAGVCVLRE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	4-[2-(2-amino-4-methyl-1H-1,3-benzimidazol-1-yl)acetamido]-N-benzyl-3-chloro-2-methylbenzamide
formula_weight	461.9 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	366

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6. Citations (1)

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length_a	79.790 Å
length_b	79.790 Å
length_c	76.890 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	1.286 Å
resolution_low	56.484 Å
r_factor	—
r_work	0.1507
r_free	0.1701

fit	/app/data/saxs_computation/y8/9y8s/9y8s.fit
pddf	/app/data/pr_computation/y8/9y8s/9y8s.pr.out
profile	/app/data/saxs_computation/y8/9y8s/9y8s.dat

Crystal structure of the Kelch domain of human KLHL12 with compound 9k

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