9awy

;Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with 3-(2-(4-(3-ethyl-3-phenylpyrrolidin-1-yl)-6-methyl-2-oxopyridin-1(2H)-yl)ethyl)-8-(imidazo[1,5-a]pyrazin-8-yl)-1,3,8-triazaspiro[4.5]decan-2-one ;

Method: X-RAY DIFFRACTION D_max: 123.8 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	9awy
沉积日期 deposition_date	2024-03-05
结构标题 title	;Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with 3-(2-(4-(3-ethyl-3-phenylpyrrolidin-1-yl)-6-methyl-2-oxopyridin-1(2H)-yl)ethyl)-8-(imidazo[1,5-a]pyrazin-8-yl)-1,3,8-triazaspiro[4.5]decan-2-one ;
关键词 keywords	Kinetic Stabilizer, Amyloid, Light Chain, Dimer, IMMUNE SYSTEM; IMMUNE SYSTEM
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	36.12 Å
回转半径 Rg (电子) rg_electron	35.53 Å
零角强度 I(0) i0	135024000.00
分子量 molecular_weight	89853.0 kDa
排除体积 excluded_volume	110970 Å³
包络体积 envelope_volume	149710 Å³
水化壳体积 shell_volume	37016 Å³
包络直径 envelope_diameter	125.9 Å
壳层 Rg shell_rg	39.66 Å
包络 Rg envelope_rg	34.69 Å
形状 Rg shape_rg	35.41 Å
总 Rg total_rg	36.19 Å
总原子数 total_atoms	12363
残基数 n_residues	847
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	123.8 Å
Rg (实空间) rg_real	36.29 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	1.3500e+08
I(0) 误差 (实空间) i0_real_error	2.4640e+06
Rg (倒空间) rg_reciprocal	36.19 Å
I(0) (倒空间) i0_reciprocal	135000000.0000
解质量估计 total_estimate	0.8694
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	39.4 Å
偏度 Skewness skewness	0.411
峰度 Kurtosis kurtosis	-0.395
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13330000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.866; Smooth: 0.839

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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	H9 Immunoglobulin Light Chain
分子量 formula_weight	22549.7 kDa
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	13247

QSALTQPPSASGSPGQSVTISCTGTSSDVGGSDSVSWYQQHPGKAPKLIIYEVSQRPSGVPNRFSGSKSGNTASLTVSGLQAEDDADYYCSSYGGDNNLFFGGGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	;3-(2-{4-[(3R)-3-ethyl-3-phenylpyrrolidin-1-yl]-6-methyl-2-oxopyridin-1(2H)-yl}ethyl)-8-[(4R)-imidazo[1,5-a]pyrazin-8-yl]-1,3,8-triazaspiro[4.5]decan-2-one ;
分子量 formula_weight	580.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	884

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7. 引用文献 (1)

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晶胞边长 a length_a	46.815 Å
晶胞边长 b length_b	63.593 Å
晶胞边长 c length_c	87.432 Å
晶胞夹角 α angle_alpha	84.37 °
晶胞夹角 β angle_beta	85.39 °
晶胞夹角 γ angle_gamma	80.08 °
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	triclinic

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	48.730 Å
R 因子 r_factor	0.2202
R_work r_work	0.2181
R_free r_free	0.2607

fit	/app/data/saxs_computation/aw/9awy/9awy.fit
pddf	/app/data/pr_computation/aw/9awy/9awy.pr.out
profile	/app/data/saxs_computation/aw/9awy/9awy.dat

;Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with 3-(2-(4-(3-ethyl-3-phenylpyrrolidin-1-yl)-6-methyl-2-oxopyridin-1(2H)-yl)ethyl)-8-(imidazo[1,5-a]pyrazin-8-yl)-1,3,8-triazaspiro[4.5]decan-2-one ;

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