8ekx

Structure of MBP-Mcl-1 in complex with MIK665

Method: X-RAY DIFFRACTION D_max: 84.9 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	8ekx
沉积日期 deposition_date	2022-09-22
结构标题 title	Structure of MBP-Mcl-1 in complex with MIK665
关键词 keywords	MBP-Mcl-1 fusion protein, apoptosis, MIK665; APOPTOSIS
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	26.19 Å
回转半径 Rg (电子) rg_electron	25.23 Å
零角强度 I(0) i0	53301100.00
分子量 molecular_weight	58119.0 kDa
排除体积 excluded_volume	73273 Å³
包络体积 envelope_volume	86717 Å³
水化壳体积 shell_volume	28945 Å³
包络直径 envelope_diameter	87.3 Å
壳层 Rg shell_rg	32.19 Å
包络 Rg envelope_rg	25.22 Å
形状 Rg shape_rg	25.20 Å
总 Rg total_rg	26.11 Å
总原子数 total_atoms	4105
残基数 n_residues	516
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	84.9 Å
Rg (实空间) rg_real	26.15 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	5.3300e+07
I(0) 误差 (实空间) i0_real_error	7.9060e+05
Rg (倒空间) rg_reciprocal	26.16 Å
I(0) (倒空间) i0_reciprocal	53300000.0000
解质量估计 total_estimate	0.8980
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	27.8 Å
偏度 Skewness skewness	0.297
峰度 Kurtosis kurtosis	-0.452
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	17250000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.983

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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 (4)

Entity 1 polymer

描述 description	Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1
分子量 formula_weight	59136.9 kDa
突变 mutation	K194A,K197A,R201A
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	4655

MAHHHHHHENLYFQGKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTGSELYRQSLEIISRYLREQATGAADTAPMGASGATSRKALETLRRVGDGVQRNHETAFQGMLRKLDIKNEDDVKSLSRVMIHVFSDGVTNWGRIVTLISFGAFVAKHLKTINQESCIEPLAESITDVLVRTKRDWLVKQRGWDGFVEFFHV

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 branched

描述 description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	;(2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-[2-[[2-(2-methoxyphenyl)pyrimidin-4-yl]methoxy]phenyl]propanoic acid ;
分子量 formula_weight	875.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	550

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7. 引用文献 (1)

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晶胞边长 a length_a	97.362 Å
晶胞边长 b length_b	136.889 Å
晶胞边长 c length_c	38.609 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 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.550 Å
最低分辨率 resolution_low	68.440 Å
R 因子 r_factor	0.1872
R_work r_work	0.1858
R_free r_free	0.2139

fit	/app/data/saxs_computation/ek/8ekx/8ekx.fit
pddf	/app/data/pr_computation/ek/8ekx/8ekx.pr.out
profile	/app/data/saxs_computation/ek/8ekx/8ekx.dat

Structure of MBP-Mcl-1 in complex with MIK665

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