SAXSdb — 1ft4

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ft4
沉积日期 deposition_date	2000-09-11
结构标题 title	PHOTOCHEMICALLY-ENHANCED BINDING OF SMALL MOLECULES TO THE TUMOR NECROSIS FACTOR RECEPTOR-1
关键词 keywords	BINDING PROTEIN, CYTOKINE, SIGNALING PROTEIN; SIGNALING PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	26.12 Å
回转半径 Rg (电子) rg_electron	25.74 Å
零角强度 I(0) i0	22819900.00
分子量 molecular_weight	32356.0 kDa
排除体积 excluded_volume	38602 Å³
包络体积 envelope_volume	55582 Å³
水化壳体积 shell_volume	18993 Å³
包络直径 envelope_diameter	85.2 Å
壳层 Rg shell_rg	31.57 Å
包络 Rg envelope_rg	25.04 Å
形状 Rg shape_rg	25.76 Å
总 Rg total_rg	26.35 Å
总原子数 total_atoms	2232
残基数 n_residues	282
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	83.5 Å
Rg (实空间) rg_real	26.27 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	2.2820e+07
I(0) 误差 (实空间) i0_real_error	3.9790e+05
Rg (倒空间) rg_reciprocal	26.22 Å
I(0) (倒空间) i0_reciprocal	22820000.0000
解质量估计 total_estimate	0.8881
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	30.1 Å
偏度 Skewness skewness	0.371
峰度 Kurtosis kurtosis	-0.483
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	879900.0000
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: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.850; Smooth: 0.824

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (2)

▼

6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d1ft4a1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.1 — TNF receptor-like

结构域编号 domain_id	d1ft4a2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.1 — TNF receptor-like

结构域编号 domain_id	d1ft4a3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.1 — TNF receptor-like

结构域编号 domain_id	d1ft4a4
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1ft4b1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.1 — TNF receptor-like

结构域编号 domain_id	d1ft4b2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.1 — TNF receptor-like

结构域编号 domain_id	d1ft4b3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.24 — TNF receptor-like
超家族 Superfamily superfamily	g.24.1 — TNF receptor-like
家族 Family family	g.24.1.1 — TNF receptor-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1ft4A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

结构域编号 domain_id	1ft4A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

结构域编号 domain_id	1ft4B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

结构域编号 domain_id	1ft4B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

▶

7. 引用文献 (3)

▶

晶胞边长 a length_a	67.800 Å
晶胞边长 b length_b	67.800 Å
晶胞边长 c length_c	190.000 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	16

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	—
R_work r_work	0.2740
R_free r_free	—

描述 description	SOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1
分子量 formula_weight	18335.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	2232

PHOTOCHEMICALLY-ENHANCED BINDING OF SMALL MOLECULES TO THE TUMOR NECROSIS FACTOR RECEPTOR-1

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

6. 折叠分类 (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

CATH v4.4 (4 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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

描述 description	5-(3-MORPHOLIN-4-YL-PROPYL)-2-(3-NITRO-PHENYL)-4-THIOXO-4,5-DIHYDRO-1-THIA-3B,5-DIAZA-CYCLOPENTA[A]PENTALEN-6-ONE
分子量 formula_weight	456.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

fit	/app/data/saxs_computation/ft/1ft4/1ft4.fit
pddf	/app/data/pr_computation/ft/1ft4/1ft4.pr.out
profile	/app/data/saxs_computation/ft/1ft4/1ft4.dat