9ftn

Crystal Structure of Autotaxin (ENPP2) with Type VI Inhibitor, a Novel Class of Inhibitors with Three-Point Lock Binding Mode

Method: X-RAY DIFFRACTION D_max: 103.0 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	9ftn
沉积日期 deposition_date	2024-06-25
结构标题 title	Crystal Structure of Autotaxin (ENPP2) with Type VI Inhibitor, a Novel Class of Inhibitors with Three-Point Lock Binding Mode
关键词 keywords	;Type VI, Inhibitor, Complex, Ectonucleotide Pyrophosphatase/Phosphodiesterase 2, lysophospholipase D (lysoPLD), lysophosphatidic acid (LPA), 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	30.37 Å
回转半径 Rg (电子) rg_electron	29.46 Å
零角强度 I(0) i0	138759000.00
分子量 molecular_weight	91759.0 kDa
排除体积 excluded_volume	113820 Å³
包络体积 envelope_volume	136700 Å³
水化壳体积 shell_volume	38677 Å³
包络直径 envelope_diameter	109.0 Å
壳层 Rg shell_rg	36.40 Å
包络 Rg envelope_rg	29.80 Å
形状 Rg shape_rg	29.38 Å
总 Rg total_rg	30.32 Å
总原子数 total_atoms	12589
残基数 n_residues	778
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	103.0 Å
Rg (实空间) rg_real	30.45 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	1.3880e+08
I(0) 误差 (实空间) i0_real_error	2.1520e+06
Rg (倒空间) rg_reciprocal	30.42 Å
I(0) (倒空间) i0_reciprocal	138800000.0000
解质量估计 total_estimate	0.8664
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	33.7 Å
偏度 Skewness skewness	0.471
峰度 Kurtosis kurtosis	-0.163
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	23770000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.902

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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 (8)

Entity 1 polymer

描述 description	Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
分子量 formula_weight	92875.4 kDa
EC 编号 ec_number	3.1.4.39
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	12963

GSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDDKVEPKNKLEELNKRLHTKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYESEI

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	nat
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	2

Entity 4 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	IODIDE ION
分子量 formula_weight	126.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	;3-(3-((4-(4-fluorophenyl)thiazol-2-yl)(methyl)amino)-6-(1-(methylsulfonyl)piperidin-4-yl)imidazo[1,2-b]pyridazin-2-yl)-N-(2-oxo-2,3-dihydrobenzo[d]oxazol-6-yl)propenamide ;
分子量 formula_weight	690.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	THIOCYANATE ION
分子量 formula_weight	58.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 8 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	127

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7. 引用文献 (1)

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晶胞边长 a length_a	53.935 Å
晶胞边长 b length_b	63.558 Å
晶胞边长 c length_c	70.599 Å
晶胞夹角 α angle_alpha	98.99 °
晶胞夹角 β angle_beta	105.21 °
晶胞夹角 γ angle_gamma	99.65 °
晶胞分子数 Z z_pdb	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	44.166 Å
R 因子 r_factor	—
R_work r_work	0.2066
R_free r_free	0.2681

fit	/app/data/saxs_computation/ft/9ftn/9ftn.fit
pddf	/app/data/pr_computation/ft/9ftn/9ftn.pr.out
profile	/app/data/saxs_computation/ft/9ftn/9ftn.dat