9c94

Crystal structure of menin in complex with inhibitor compound 20

Method: X-RAY DIFFRACTION D_max: 107.0 Å Quality: REASONABLE

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	9c94
沉积日期 deposition_date	2024-06-13
结构标题 title	Crystal structure of menin in complex with inhibitor compound 20
关键词 keywords	PROTEIN BINDING, PROTEIN BINDING-INHIBITOR COMPLEX; PROTEIN BINDING/INHIBITOR
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	31.58 Å
回转半径 Rg (电子) rg_electron	30.99 Å
零角强度 I(0) i0	332842000.00
分子量 molecular_weight	98706.0 kDa
排除体积 excluded_volume	95977 Å³
包络体积 envelope_volume	167400 Å³
水化壳体积 shell_volume	44839 Å³
包络直径 envelope_diameter	112.9 Å
壳层 Rg shell_rg	38.37 Å
包络 Rg envelope_rg	30.61 Å
形状 Rg shape_rg	30.99 Å
总 Rg total_rg	31.43 Å
总原子数 total_atoms	7501
残基数 n_residues	938
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	107.0 Å
Rg (实空间) rg_real	31.54 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	3.3280e+08
I(0) 误差 (实空间) i0_real_error	5.0580e+06
Rg (倒空间) rg_reciprocal	31.56 Å
I(0) (倒空间) i0_reciprocal	332800000.0000
解质量估计 total_estimate	0.6613
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	38.5 Å
偏度 Skewness skewness	0.359
峰度 Kurtosis kurtosis	-0.207
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	41400000.0000
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: 0.814; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 1.000; Smooth: 0.964

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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	Menin
分子量 formula_weight	57010.5 kDa
突变 mutation	A5T
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,B
原子数 atom_count	8159

MHHHHHHSSGRENLYFQGSGLKTAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVIPTNVPELTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGEERPGEQSQGTQSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRITFQSEKMKGMKELLVATKINSSAIKLQLTAQS

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

Entity 2 non-polymer

描述 description	;{5-fluoro-2-[(5-{7-[(1-methylcyclopropyl)methyl]-2,7-diazaspiro[3.5]nonan-2-yl}-1,2,4-triazin-6-yl)oxy]phenyl}[(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]methanone ;
分子量 formula_weight	522.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	609

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7. 引用文献 (1)

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晶胞边长 a length_a	56.758 Å
晶胞边长 b length_b	87.476 Å
晶胞边长 c length_c	194.610 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.980 Å
最低分辨率 resolution_low	54.490 Å
R 因子 r_factor	0.1797
R_work r_work	0.1780
R_free r_free	0.2117

fit	/app/data/saxs_computation/c9/9c94/9c94.fit
pddf	/app/data/pr_computation/c9/9c94/9c94.pr.out
profile	/app/data/saxs_computation/c9/9c94/9c94.dat

Crystal structure of menin in complex with inhibitor compound 20

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