9diz

;Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM959 (6-cyclopropyl-2,4-dimethyl-3-((6-(trifluoromethyl)pyridin-3-yl)methyl)-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one) ;

Method: X-RAY DIFFRACTION D_max: 66.0 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	9diz
沉积日期 deposition_date	2024-09-06
结构标题 title	;Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM959 (6-cyclopropyl-2,4-dimethyl-3-((6-(trifluoromethyl)pyridin-3-yl)methyl)-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one) ;
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	20.75 Å
回转半径 Rg (电子) rg_electron	19.64 Å
零角强度 I(0) i0	29871400.00
分子量 molecular_weight	43088.0 kDa
排除体积 excluded_volume	54395 Å³
包络体积 envelope_volume	61559 Å³
水化壳体积 shell_volume	24906 Å³
包络直径 envelope_diameter	68.6 Å
壳层 Rg shell_rg	27.32 Å
包络 Rg envelope_rg	20.09 Å
形状 Rg shape_rg	19.64 Å
总 Rg total_rg	20.62 Å
总原子数 total_atoms	6069
残基数 n_residues	374
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	66.0 Å
Rg (实空间) rg_real	20.58 Å
Rg 误差 (实空间) rg_real_error	0.37 Å
I(0) (实空间) i0_real	2.9870e+07
I(0) 误差 (实空间) i0_real_error	3.6880e+05
Rg (倒空间) rg_reciprocal	20.62 Å
I(0) (倒空间) i0_reciprocal	29870000.0000
解质量估计 total_estimate	0.8062
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	26.8 Å
偏度 Skewness skewness	0.078
峰度 Kurtosis kurtosis	-0.462
角度范围 angular_range	— – 0.3850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10900000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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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 (4)

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	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6069

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	6-cyclopropyl-2,4-dimethyl-3-{[6-(trifluoromethyl)pyridin-3-yl]methyl}-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one
分子量 formula_weight	362.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	1

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	1

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7. 引用文献 (2)

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晶胞边长 a length_a	85.224 Å
晶胞边长 b length_b	85.224 Å
晶胞边长 c length_c	139.888 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 64
空间群编号 int_tables_number	172
晶系 crystal_system	hexagonal

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	40.760 Å
R 因子 r_factor	0.1976
R_work r_work	0.1936
R_free r_free	0.2283

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

;Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM959 (6-cyclopropyl-2,4-dimethyl-3-((6-(trifluoromethyl)pyridin-3-yl)methyl)-2,6-dihydro-7H-pyrazolo[3,4-c]pyridin-7-one) ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

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

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

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction