SAXSdb — 8v8j

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8v8j
沉积日期 deposition_date	2023-12-05
结构标题 title	PI3Ka H1047R co-crystal structure with inhibitors in two cryptic pockets (compounds 4 and 5).
关键词 keywords	H1047R, PI3K, PI3Ka, SIGNALING PROTEIN; SIGNALING PROTEIN
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	51.48 Å
回转半径 Rg (电子) rg_electron	51.42 Å
零角强度 I(0) i0	1238430000.00
分子量 molecular_weight	297510.0 kDa
排除体积 excluded_volume	374000 Å³
包络体积 envelope_volume	537680 Å³
水化壳体积 shell_volume	86922 Å³
包络直径 envelope_diameter	176.3 Å
壳层 Rg shell_rg	54.61 Å
包络 Rg envelope_rg	50.83 Å
形状 Rg shape_rg	51.44 Å
总 Rg total_rg	51.47 Å
总原子数 total_atoms	20898
残基数 n_residues	2508
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	171.0 Å
Rg (实空间) rg_real	51.54 Å
Rg 误差 (实空间) rg_real_error	1.28 Å
I(0) (实空间) i0_real	1.2380e+09
I(0) 误差 (实空间) i0_real_error	2.3590e+07
Rg (倒空间) rg_reciprocal	51.42 Å
I(0) (倒空间) i0_reciprocal	1238000000.0000
解质量估计 total_estimate	0.8762
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	49.6 Å
偏度 Skewness skewness	0.329
峰度 Kurtosis kurtosis	-0.609
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	172600000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.804

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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 (5)

Entity 1 polymer

描述 description	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
分子量 formula_weight	124810.4 kDa
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,C
原子数 atom_count	20898

AMGSMPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDARHGGWTTKMDWIFHTIKQHALN

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	Trichoplusia ni

Entity 2 polymer

描述 description	Phosphatidylinositol 3-kinase regulatory subunit alpha
分子量 formula_weight	33667.0 kDa
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	B,D

MNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGN

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	Trichoplusia ni

Entity 3 non-polymer

描述 description	2-({(1R)-1-[2-(4,4-dimethylpiperidin-1-yl)-3,6-dimethyl-4-oxo-4H-1-benzopyran-8-yl]ethyl}amino)benzoic acid
分子量 formula_weight	448.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	N-{(3S)-3-(2-methylphenyl)-6-[(oxetan-3-yl)amino]-1-oxo-2,3-dihydro-1H-isoindol-4-yl}-1-benzothiophene-3-carboxamide
分子量 formula_weight	469.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	(2S)-N~1~-[(4P)-2-tert-butyl-4'-methyl[4,5'-bi-1,3-thiazol]-2'-yl]pyrrolidine-1,2-dicarboxamide
分子量 formula_weight	393.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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7. 引用文献 (1)

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晶胞边长 a length_a	236.940 Å
晶胞边长 b length_b	158.480 Å
晶胞边长 c length_c	121.600 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.83 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.350 Å
最低分辨率 resolution_low	43.470 Å
R 因子 r_factor	0.2112
R_work r_work	0.2091
R_free r_free	0.2513

fit	/app/data/saxs_computation/v8/8v8j/8v8j.fit
pddf	/app/data/pr_computation/v8/8v8j/8v8j.pr.out
profile	/app/data/saxs_computation/v8/8v8j/8v8j.dat

PI3Ka H1047R co-crystal structure with inhibitors in two cryptic pockets (compounds 4 and 5).

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

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)