9ggh

;Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) in complex with N-((6-(Hydroxyamino)-6-oxohexyl)oxy)-4-(4-(pyrrolidin-1-yl)phenyl)thiazole-2-carboxamide ;

Method: X-RAY DIFFRACTION D_max: 63.8 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	9ggh
沉积日期 deposition_date	2024-08-13
结构标题 title	;Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) in complex with N-((6-(Hydroxyamino)-6-oxohexyl)oxy)-4-(4-(pyrrolidin-1-yl)phenyl)thiazole-2-carboxamide ;
关键词 keywords	Histone deacetylase, zinc enzyme, inhibitor, HYDROLASE; HYDROLASE
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	19.77 Å
回转半径 Rg (电子) rg_electron	18.84 Å
零角强度 I(0) i0	52760200.00
分子量 molecular_weight	37232.0 kDa
排除体积 excluded_volume	35526 Å³
包络体积 envelope_volume	53983 Å³
水化壳体积 shell_volume	22943 Å³
包络直径 envelope_diameter	65.5 Å
壳层 Rg shell_rg	26.34 Å
包络 Rg envelope_rg	19.27 Å
形状 Rg shape_rg	18.84 Å
总 Rg total_rg	19.49 Å
总原子数 total_atoms	2792
残基数 n_residues	354
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	63.8 Å
Rg (实空间) rg_real	19.62 Å
Rg 误差 (实空间) rg_real_error	0.27 Å
I(0) (实空间) i0_real	5.2760e+07
I(0) 误差 (实空间) i0_real_error	6.3950e+05
Rg (倒空间) rg_reciprocal	19.64 Å
I(0) (倒空间) i0_reciprocal	52760000.0000
解质量估计 total_estimate	0.8855
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.1 Å
偏度 Skewness skewness	0.142
峰度 Kurtosis kurtosis	-0.424
角度范围 angular_range	— – 0.4000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12110000.0000
实空间数据点数 n_real_points	72
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999

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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	Histone deacetylase 6
分子量 formula_weight	40285.5 kDa
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	2828

SNAGGSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLR

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	zebrafish
NCBI 分类编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	~{N}-[6-(oxidanylamino)-6-oxidanylidene-hexoxy]-4-(4-pyrrolidin-1-ylphenyl)-1,3-thiazolidine-2-carboxamide
分子量 formula_weight	418.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 4 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	29

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7. 引用文献 (1)

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晶胞边长 a length_a	42.711 Å
晶胞边长 b length_b	87.033 Å
晶胞边长 c length_c	178.864 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.140 Å
最低分辨率 resolution_low	44.760 Å
R 因子 r_factor	0.2094
R_work r_work	0.2075
R_free r_free	0.2472

fit	/app/data/saxs_computation/gg/9ggh/9ggh.fit
pddf	/app/data/pr_computation/gg/9ggh/9ggh.pr.out
profile	/app/data/saxs_computation/gg/9ggh/9ggh.dat

;Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) in complex with N-((6-(Hydroxyamino)-6-oxohexyl)oxy)-4-(4-(pyrrolidin-1-yl)phenyl)thiazole-2-carboxamide ;

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