9dik

;Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM681 (N-cyclopropyl-1,4-dimethyl-5-((6-(trifluoromethyl)pyridin-3-yl)methyl)-1H-pyrazole-3-carboxamide) ;

Method: X-RAY DIFFRACTION D_max: 98.4 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9dik
沉积日期 deposition_date	2024-09-05
结构标题 title	;Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM681 (N-cyclopropyl-1,4-dimethyl-5-((6-(trifluoromethyl)pyridin-3-yl)methyl)-1H-pyrazole-3-carboxamide) ;
关键词 keywords	inhibitor, Alpha-Beta Barrel, OXIDOREDUCTASE, Flavoprotein, OXIDOREDUCTASE-INHIBITOR complex; OXIDOREDUCTASE/INHIBITOR
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	29.80 Å
回转半径 Rg (电子) rg_electron	29.45 Å
零角强度 I(0) i0	109785000.00
分子量 molecular_weight	85546.0 kDa
排除体积 excluded_volume	108150 Å³
包络体积 envelope_volume	128660 Å³
水化壳体积 shell_volume	36351 Å³
包络直径 envelope_diameter	103.0 Å
壳层 Rg shell_rg	36.72 Å
包络 Rg envelope_rg	29.56 Å
形状 Rg shape_rg	29.46 Å
总 Rg total_rg	30.09 Å
总原子数 total_atoms	12068
残基数 n_residues	742
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	98.4 Å
Rg (实空间) rg_real	29.85 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	1.0980e+08
I(0) 误差 (实空间) i0_real_error	1.6420e+06
Rg (倒空间) rg_reciprocal	29.83 Å
I(0) (倒空间) i0_reciprocal	109800000.0000
解质量估计 total_estimate	0.8791
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	31.6 Å
偏度 Skewness skewness	0.396
峰度 Kurtosis kurtosis	-0.467
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0003
最高正则化参数 α highest_alpha	42130000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.968

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	Dihydroorotate dehydrogenase (quinone), mitochondrial
分子量 formula_weight	45385.9 kDa
EC 编号 ec_number	1.3.5.2
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	12372

MGHHHHHHAENLYFQGADPFESYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDEFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRKHSKS

来源 Source

来源生物 organism	Plasmodium falciparum 3D7
NCBI 分类编号 ncbi_taxonomy_id	36329
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	N-cyclopropyl-1,4-dimethyl-5-{[6-(trifluoromethyl)pyridin-3-yl]methyl}-1H-pyrazole-3-carboxamide
分子量 formula_weight	338.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	FLAVIN MONONUCLEOTIDE
分子量 formula_weight	456.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	6-[bis(oxidanyl)methyl]-5~{H}-pyrimidine-2,4-dione
分子量 formula_weight	158.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	255

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7. 引用文献 (2)

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晶胞边长 a length_a	68.539 Å
晶胞边长 b length_b	107.979 Å
晶胞边长 c length_c	157.835 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	40.960 Å
R 因子 r_factor	0.1770
R_work r_work	0.1760
R_free r_free	0.2098

fit	/app/data/saxs_computation/di/9dik/9dik.fit
pddf	/app/data/pr_computation/di/9dik/9dik.pr.out
profile	/app/data/saxs_computation/di/9dik/9dik.dat