8rqo

Human thyroid hormone receptor alpha ligand binding domain in complex with beta-selective agonist ALG-055009

Method: X-RAY DIFFRACTION D_max: 67.1 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	8rqo
沉积日期 deposition_date	2024-01-18
结构标题 title	Human thyroid hormone receptor alpha ligand binding domain in complex with beta-selective agonist ALG-055009
关键词 keywords	;thyroid receptor beta, thyroid receptor alpha, nuclear receptors, thyroid receptor agonist, thyroid receptor ligand, structure-based drug design, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
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	20.21 Å
回转半径 Rg (电子) rg_electron	19.16 Å
零角强度 I(0) i0	15834600.00
分子量 molecular_weight	29778.0 kDa
排除体积 excluded_volume	37187 Å³
包络体积 envelope_volume	43824 Å³
水化壳体积 shell_volume	19306 Å³
包络直径 envelope_diameter	71.3 Å
壳层 Rg shell_rg	25.39 Å
包络 Rg envelope_rg	19.71 Å
形状 Rg shape_rg	19.13 Å
总 Rg total_rg	20.11 Å
总原子数 total_atoms	2085
残基数 n_residues	257
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	67.1 Å
Rg (实空间) rg_real	20.17 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.5830e+07
I(0) 误差 (实空间) i0_real_error	1.9610e+05
Rg (倒空间) rg_reciprocal	20.18 Å
I(0) (倒空间) i0_reciprocal	15830000.0000
解质量估计 total_estimate	0.6343
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	24.9 Å
偏度 Skewness skewness	0.318
峰度 Kurtosis kurtosis	-0.289
角度范围 angular_range	— – 0.3950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3744000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 0.260; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	Isoform Alpha-1 of Thyroid hormone receptor alpha
分子量 formula_weight	32251.1 kDa
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	2099

MGSSHHHHHHSSGLVPRGSHMEEMIRSLQQRPEPTPEEWDLIHIATEAHRSTNAQGSHWKQRRKFLPDDIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLCVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEVFEDQEV

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	6-azanyl-2-[3,5-bis(chloranyl)-4-[(6-oxidanylidene-5-propan-2-yl-1~{H}-pyridazin-3-yl)oxy]phenyl]-1,2,4-triazine-3,5-dione
分子量 formula_weight	425.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 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	14

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7. 引用文献 (1)

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晶胞边长 a length_a	110.199 Å
晶胞边长 b length_b	110.199 Å
晶胞边长 c length_c	134.579 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.740 Å
最低分辨率 resolution_low	95.450 Å
R 因子 r_factor	0.1953
R_work r_work	0.1935
R_free r_free	0.2278

fit	/app/data/saxs_computation/rq/8rqo/8rqo.fit
pddf	/app/data/pr_computation/rq/8rqo/8rqo.pr.out
profile	/app/data/saxs_computation/rq/8rqo/8rqo.dat

Human thyroid hormone receptor alpha ligand binding domain in complex with beta-selective agonist ALG-055009

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