8ow2

Crystal structure of the p110alpha catalytic subunit from homo sapiens in complex with activator 1938

Method: X-RAY DIFFRACTION D_max: 106.1 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	8ow2
沉积日期 deposition_date	2023-04-26
结构标题 title	Crystal structure of the p110alpha catalytic subunit from homo sapiens in complex with activator 1938
关键词 keywords	cardioprotection, neuroregeneration, pi3k, kinase, TRANSFERASE; TRANSFERASE
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	31.67 Å
回转半径 Rg (电子) rg_electron	30.61 Å
零角强度 I(0) i0	169548000.00
分子量 molecular_weight	104610.0 kDa
排除体积 excluded_volume	131450 Å³
包络体积 envelope_volume	166430 Å³
水化壳体积 shell_volume	44371 Å³
包络直径 envelope_diameter	116.3 Å
壳层 Rg shell_rg	38.36 Å
包络 Rg envelope_rg	30.88 Å
形状 Rg shape_rg	30.58 Å
总 Rg total_rg	31.36 Å
总原子数 total_atoms	14658
残基数 n_residues	895
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	106.1 Å
Rg (实空间) rg_real	31.53 Å
Rg 误差 (实空间) rg_real_error	0.72 Å
I(0) (实空间) i0_real	1.6950e+08
I(0) 误差 (实空间) i0_real_error	2.6950e+06
Rg (倒空间) rg_reciprocal	31.59 Å
I(0) (倒空间) i0_reciprocal	169600000.0000
解质量估计 total_estimate	0.8848
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	40.3 Å
偏度 Skewness skewness	0.221
峰度 Kurtosis kurtosis	-0.393
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	46700000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

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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 (3)

Entity 1 polymer

描述 description	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
分子量 formula_weight	109969.1 kDa
EC 编号 ec_number	2.7.1.137,2.7.1.153,2.7.11.1
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	14702

GSVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKDTPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	1-[7-[[2-[[4-(4-ethylpiperazin-1-yl)phenyl]amino]pyridin-4-yl]amino]-2,3-dihydroindol-1-yl]ethanone
分子量 formula_weight	456.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	36

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	8ow2A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	150 — C2 domain

结构域编号 domain_id	8ow2A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	70 — Phosphatidylinositol 3-kinase, accessory domain (PIK)

结构域编号 domain_id	8ow2A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1070 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5
同源超家族 H-superfamily homologous superfamily	11 — Phosphatidylinositol 3-/4-kinase, catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	58.720 Å
晶胞边长 b length_b	134.880 Å
晶胞边长 c length_c	144.770 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	4

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	2.570 Å
最低分辨率 resolution_low	50.460 Å
R 因子 r_factor	0.2158
R_work r_work	0.2128
R_free r_free	0.2714

fit	/app/data/saxs_computation/ow/8ow2/8ow2.fit
pddf	/app/data/pr_computation/ow/8ow2/8ow2.pr.out
profile	/app/data/saxs_computation/ow/8ow2/8ow2.dat

Crystal structure of the p110alpha catalytic subunit from homo sapiens in complex with activator 1938

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