9d00

HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 53

Method: X-RAY DIFFRACTION D_max: 123.3 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	9d00
沉积日期 deposition_date	2024-08-05
结构标题 title	HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 53
关键词 keywords	Kinase, 3D domain swap, inactive state, 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	39.16 Å
回转半径 Rg (电子) rg_electron	38.61 Å
零角强度 I(0) i0	473447000.00
分子量 molecular_weight	119780.0 kDa
排除体积 excluded_volume	116660 Å³
包络体积 envelope_volume	222470 Å³
水化壳体积 shell_volume	47521 Å³
包络直径 envelope_diameter	129.7 Å
壳层 Rg shell_rg	45.51 Å
包络 Rg envelope_rg	37.20 Å
形状 Rg shape_rg	38.60 Å
总 Rg total_rg	38.92 Å
总原子数 total_atoms	9105
残基数 n_residues	1137
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	123.3 Å
Rg (实空间) rg_real	39.00 Å
Rg 误差 (实空间) rg_real_error	1.40 Å
I(0) (实空间) i0_real	4.7340e+08
I(0) 误差 (实空间) i0_real_error	9.3600e+06
Rg (倒空间) rg_reciprocal	39.11 Å
I(0) (倒空间) i0_reciprocal	473500000.0000
解质量估计 total_estimate	0.8890
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	55.5 Å
偏度 Skewness skewness	0.090
峰度 Kurtosis kurtosis	-0.573
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	34600000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.874

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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	Mitogen-activated protein kinase kinase kinase kinase 1
分子量 formula_weight	34504.9 kDa
EC 编号 ec_number	2.7.11.1
突变 mutation	T165E, S171E
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	9632

GSMDVVDPDIFNRDPRDHYDLLQRLGGGTYGEVFKARDKVSGDLVALKMVKMEPDDDVSTLQKEILILKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIYQVTGSLSELQISYVCREVLQGLAYLHSQKKIHRDIKGANILINDAGEVRLADFGISAQIGAELARRLEFIGTPYWMAPEVAAVALKGGYNELCDIWSLGITAIELAELQPPLFDVHPLRVLFLMTKSGYQPPRLKEKGKWSAAFHNFIKVTLTKSPKKRPSATKMLSHQLVSQPGLNRGLILDLLDKLKNPGKGPSIGDIEDEE

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	Spodoptera frugiperda

Entity 2 non-polymer

描述 description	4-[(1R)-1-aminopropyl]-6-methoxy-2-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}-2,3-dihydro-1H-isoindol-1-one
分子量 formula_weight	406.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	527

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7. 引用文献 (1)

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晶胞边长 a length_a	56.780 Å
晶胞边长 b length_b	80.330 Å
晶胞边长 c length_c	84.090 Å
晶胞夹角 α angle_alpha	103.45 °
晶胞夹角 β angle_beta	106.49 °
晶胞夹角 γ angle_gamma	103.18 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	1.951 Å
最低分辨率 resolution_low	33.340 Å
R 因子 r_factor	0.2474
R_work r_work	0.2457
R_free r_free	0.2791

fit	/app/data/saxs_computation/d0/9d00/9d00.fit
pddf	/app/data/pr_computation/d0/9d00/9d00.pr.out
profile	/app/data/saxs_computation/d0/9d00/9d00.dat

HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 53

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