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9tlz

Plasmodium falciparum dihydroorotate dehydrogenase in complex with 3-hydroxy-1-methyl pyrazole derivatives

Method: X-RAY DIFFRACTION D_max: 104.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tlz
deposition_date	2025-12-11
last_revision	2026-04-01
title	Plasmodium falciparum dihydroorotate dehydrogenase in complex with 3-hydroxy-1-methyl pyrazole derivatives
keywords	;Malaria, Plasmodium falciparum, Pyrimidine biosynthesis, dihydroorotate dehydrogenase, structure-based drug design, inhibitors, 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	30.21 Å
rg_electron	30.04 Å
i0	226580000.00
molecular_weight	80681.0 kDa
excluded_volume	78195 Å³
envelope_volume	129250 Å³
shell_volume	36136 Å³
envelope_diameter	111.6 Å
shell_rg	36.76 Å
envelope_rg	30.15 Å
shape_rg	30.06 Å
total_rg	30.43 Å
total_atoms	6123
n_residues	753
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	104.1 Å
rg_real	30.32 Å
rg_real_error	0.99 Å
i0_real	2.2660e+08
i0_real_error	3.9410e+06
rg_reciprocal	30.27 Å
i0_reciprocal	226600000.0000
total_estimate	0.6624
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	30.0 Å
skewness	0.434
kurtosis	-0.415
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	46640000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.885; Smooth: 0.913

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Dihydroorotate dehydrogenase (quinone), mitochondrial
formula_weight	45852.5 kDa
ec_number	1.3.5.2
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6144

MHHHHHHSSGVDLGTENLYFQSMFESYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRKHSKS

Source

organism	Plasmodium falciparum
common_name	malaria parasite P. falciparum
ncbi_taxonomy_id	5833
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	OROTIC ACID
formula_weight	156.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	1-methyl-3-oxidanyl-5-[[[3-[pentakis(fluoranyl)-$l^{6}-sulfanyl]phenyl]amino]methyl]pyrazole-4-carboxylic acid
formula_weight	373.3 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	21

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6. Citations (1)

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length_a	52.364 Å
length_b	163.130 Å
length_c	62.656 Å
angle_alpha	90.00 °
angle_beta	107.91 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.950 Å
resolution_low	48.130 Å
r_factor	0.1934
r_work	0.1898
r_free	0.2613

fit	/app/data/saxs_computation/tl/9tlz/9tlz.fit
pddf	/app/data/pr_computation/tl/9tlz/9tlz.pr.out
profile	/app/data/saxs_computation/tl/9tlz/9tlz.dat