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9s1i

Crystal structure of human Dihydroorotate Dehydrogenase in complex with arzanol

Method: X-RAY DIFFRACTION D_max: 59.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s1i
deposition_date	2025-07-18
title	Crystal structure of human Dihydroorotate Dehydrogenase in complex with arzanol
keywords	Pyrimidine Biosynthesis, Flavoprotein, DHODH, arzanol, 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	19.88 Å
rg_electron	18.77 Å
i0	50379800.00
molecular_weight	36325.0 kDa
excluded_volume	34818 Å³
envelope_volume	54575 Å³
shell_volume	23158 Å³
envelope_diameter	61.4 Å
shell_rg	26.19 Å
envelope_rg	19.13 Å
shape_rg	18.67 Å
total_rg	19.61 Å
total_atoms	2803
n_residues	350
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	59.6 Å
rg_real	19.69 Å
rg_real_error	0.26 Å
i0_real	5.0380e+07
i0_real_error	5.6200e+05
rg_reciprocal	19.72 Å
i0_reciprocal	50380000.0000
total_estimate	0.8991
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.8 Å
skewness	0.054
kurtosis	-0.524
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	14920000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Dihydroorotate dehydrogenase (quinone), mitochondrial
formula_weight	42636.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3134

MGHHHHHHHHHHSSGHIDDDDKHMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	OROTIC ACID
formula_weight	156.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	3-[[3-ethanoyl-5-(3-methylbut-2-enyl)-2,4,6-tris(oxidanyl)phenyl]methyl]-6-ethyl-5-methyl-4-oxidanyl-pyran-2-one
formula_weight	402.4 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	286

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6. Citations (1)

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length_a	90.477 Å
length_b	90.477 Å
length_c	122.860 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	1.610 Å
resolution_low	48.340 Å
r_factor	0.1645
r_work	0.1639
r_free	0.1755

fit	/app/data/saxs_computation/s1/9s1i/9s1i.fit
pddf	/app/data/pr_computation/s1/9s1i/9s1i.pr.out
profile	/app/data/saxs_computation/s1/9s1i/9s1i.dat