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9ub2

Crystal structure of human DHODH in complex with inhibitor 006

Method: X-RAY DIFFRACTION D_max: 67.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ub2
deposition_date	2025-04-02
last_revision	2026-04-08
title	Crystal structure of human DHODH in complex with inhibitor 006
keywords	Dihydroorotate dehydrogenase (DHODH), Inhibitor, Complex, OXIDOREDUCTASE; OXIDOREDUCTASE
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	20.61 Å
rg_electron	19.53 Å
i0	54214000.00
molecular_weight	37579.0 kDa
excluded_volume	35926 Å³
envelope_volume	59847 Å³
shell_volume	24485 Å³
envelope_diameter	63.0 Å
shell_rg	27.05 Å
envelope_rg	19.82 Å
shape_rg	19.48 Å
total_rg	20.31 Å
total_atoms	2871
n_residues	363
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	67.9 Å
rg_real	20.44 Å
rg_real_error	0.47 Å
i0_real	5.4210e+07
i0_real_error	7.1600e+05
rg_reciprocal	20.47 Å
i0_reciprocal	54210000.0000
total_estimate	0.7961
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	26.6 Å
skewness	0.080
kurtosis	-0.495
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	15320000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Dihydroorotate dehydrogenase (quinone), mitochondrial
formula_weight	39725.3 kDa
ec_number	1.3.5.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2946

ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	OROTIC ACID
formula_weight	156.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	(4R)-2-[(3-cyclobutyloxy-4-phenyl-pyridin-2-yl)amino]-4,5,6,7-tetrahydro-1,3-benzothiazol-4-ol
formula_weight	393.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	75

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6. Citations (1)

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length_a	92.915 Å
length_b	92.915 Å
length_c	125.340 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	1.900 Å
resolution_low	28.980 Å
r_factor	0.2010
r_work	0.2002
r_free	0.2217

fit	/app/data/saxs_computation/ub/9ub2/9ub2.fit
pddf	/app/data/pr_computation/ub/9ub2/9ub2.pr.out
profile	/app/data/saxs_computation/ub/9ub2/9ub2.dat