9l65

A novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures

Method: X-RAY DIFFRACTION D_max: 112.9 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	9l65
沉积日期 deposition_date	2024-12-24
结构标题 title	A novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures
关键词 keywords	Inhibitors, Complex, Allosteric, 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	33.70 Å
回转半径 Rg (电子) rg_electron	33.42 Å
零角强度 I(0) i0	314473000.00
分子量 molecular_weight	95650.0 kDa
排除体积 excluded_volume	92667 Å³
包络体积 envelope_volume	161480 Å³
水化壳体积 shell_volume	41253 Å³
包络直径 envelope_diameter	115.2 Å
壳层 Rg shell_rg	38.96 Å
包络 Rg envelope_rg	33.51 Å
形状 Rg shape_rg	33.38 Å
总 Rg total_rg	33.79 Å
总原子数 total_atoms	7267
残基数 n_residues	885
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	112.9 Å
Rg (实空间) rg_real	33.81 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	3.1450e+08
I(0) 误差 (实空间) i0_real_error	5.7500e+06
Rg (倒空间) rg_reciprocal	33.74 Å
I(0) (倒空间) i0_reciprocal	314500000.0000
解质量估计 total_estimate	0.6502
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.446
峰度 Kurtosis kurtosis	-0.397
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31170000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.909; Smooth: 0.844

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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	Alpha-(1,6)-fucosyltransferase
分子量 formula_weight	57638.8 kDa
EC 编号 ec_number	2.4.1.68
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	8048

DAAQPADYKDHDGDYKDHDIDYKDDDDKRNGLGKDHEILRRRIENGAKELWFFLQSELKKLKNLEGNELQRHADEFLLDLGHHERSIMTDLYYLSQTDGAGDWREKEAKDLTELVQRRITYLQNPKDCSKAKKLVCNINKGCGYGCQLHHVVYCFMIAYGTQRTLILESQNWRYATGGWETVFRPVSETCTDRSGISTGHWSGEVKDKNVQVVELPIVDSLHPRPPYLPLAVPEDLADRLVRVHGDPAVWWVSQFVKYLIRPQPWLEKEIEEATKKLGFKHPVIGVHVRRTDKVGTEAAFHPIEEYMVHVEEHFQLLARRMQVDKKRVYLATDDPSLLKEAKTKYPNYEFISDNSISWSAGLHNRYTENSLRGVILDIHFLSQADFLVCTFSSQVCRVAYEIMQTLHPDASANFHSLDDIYYFGGQNAHNQIAIYAHQPRTADEIPMEPGDIIGVAGNHWDGYSKGVNRKLGRTGLYPSYKVREKIETVKYPTYPEAEK

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	Homo sapiens

Entity 2 non-polymer

描述 description	[2,6-bis(oxidanylidene)piperidin-1-yl] 18-(2,3-dimethylimidazol-1-ium-1-yl)octadecanoate
分子量 formula_weight	476.7 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	781

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7. 引用文献 (1)

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晶胞边长 a length_a	196.360 Å
晶胞边长 b length_b	69.220 Å
晶胞边长 c length_c	105.120 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	118.71 °
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	1.990 Å
最低分辨率 resolution_low	52.460 Å
R 因子 r_factor	0.1792
R_work r_work	0.1776
R_free r_free	0.2092

fit	/app/data/saxs_computation/l6/9l65/9l65.fit
pddf	/app/data/pr_computation/l6/9l65/9l65.pr.out
profile	/app/data/saxs_computation/l6/9l65/9l65.dat

A novel allosteric covalent inhibitory site of fucosyltransferase 8 revealed by crystal structures

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