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9vd2

Crystal Structure of kelch domain of human KEAP1 in complex with CH7286675

Method: X-RAY DIFFRACTION D_max: 56.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vd2
deposition_date	2025-06-07
last_revision	2025-10-15
title	Crystal Structure of kelch domain of human KEAP1 in complex with CH7286675
keywords	BETA-PROPELLER, KELCH REPEAT MOTIF, PROTEIN BINDIN, TRANSCRIPTION; TRANSCRIPTION
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	18.58 Å
rg_electron	17.59 Å
i0	35948400.00
molecular_weight	30335.0 kDa
excluded_volume	28891 Å³
envelope_volume	44400 Å³
shell_volume	20258 Å³
envelope_diameter	57.7 Å
shell_rg	24.74 Å
envelope_rg	17.84 Å
shape_rg	17.56 Å
total_rg	18.34 Å
total_atoms	2277
n_residues	285
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	56.2 Å
rg_real	18.42 Å
rg_real_error	0.22 Å
i0_real	3.5950e+07
i0_real_error	3.7970e+05
rg_reciprocal	18.44 Å
i0_reciprocal	35950000.0000
total_estimate	0.9008
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.6 Å
skewness	0.038
kurtosis	-0.530
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	13820000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Kelch-like ECH-associated protein 1
formula_weight	31951.8 kDa
mutation	E540A/E542A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2606

GSHMAPKVGRLIYTAGGYFRQSLSYLEAYNPSDGTWLRLADLQVPRSGLAGCVVGGLLYAVGGRNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAVGGSHGCIHHNSVERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRMITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVATATWTFVAPMKHRRSALGITVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;4-[3-[2,6-dichloro-4-(6-methoxy-2-azaspiro[3.3]heptan-2-yl)benzoyl]-2,4-dihydro-1,3-benzoxazin-8-yl]-5-fluoro-2-(3-oxa-8-azabicyclo[3.2.1]octan-8-yl)benzoic acid ;
formula_weight	682.6 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	300

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6. Citations (1)

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length_a	126.642 Å
length_b	76.410 Å
length_c	48.222 Å
angle_alpha	90.00 °
angle_beta	105.44 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.699 Å
resolution_low	32.990 Å
r_factor	0.1867
r_work	0.1854
r_free	0.2118

fit	/app/data/saxs_computation/vd/9vd2/9vd2.fit
pddf	/app/data/pr_computation/vd/9vd2/9vd2.pr.out
profile	/app/data/saxs_computation/vd/9vd2/9vd2.dat