1f9e

CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO

Method: X-RAY DIFFRACTION D_max: 119.6 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	1f9e
沉积日期 deposition_date	2000-07-10
结构标题 title	CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO
关键词 keywords	CYSTEINE PROTEASE, CASPASE-8, FLICE, MCH5, MACH, APOPTOSIS, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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	43.11 Å
回转半径 Rg (电子) rg_electron	42.43 Å
零角强度 I(0) i0	431096000.00
分子量 molecular_weight	169460.0 kDa
排除体积 excluded_volume	211280 Å³
包络体积 envelope_volume	284100 Å³
水化壳体积 shell_volume	54357 Å³
包络直径 envelope_diameter	130.0 Å
壳层 Rg shell_rg	50.06 Å
包络 Rg envelope_rg	40.65 Å
形状 Rg shape_rg	42.43 Å
总 Rg total_rg	42.80 Å
总原子数 total_atoms	11879
残基数 n_residues	1470
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	119.6 Å
Rg (实空间) rg_real	42.89 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	4.3110e+08
I(0) 误差 (实空间) i0_real_error	8.0840e+06
Rg (倒空间) rg_reciprocal	43.11 Å
I(0) (倒空间) i0_reciprocal	431200000.0000
解质量估计 total_estimate	0.6276
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	71.1 Å
偏度 Skewness skewness	-0.086
峰度 Kurtosis kurtosis	-0.911
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	42860000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 0.083; Positv: 1.000; Valcen: 0.985; Smooth: 0.098

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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	Caspase-8 subunit p18
分子量 formula_weight	17417.0 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G,I,K
原子数 atom_count	11926

LDKVYQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHHDCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVFFIQACQGDNYQKGIPVETD

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 polymer

描述 description	Caspase-8 subunit p10
分子量 formula_weight	10273.7 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H,J,L

TRYIPDEADFLLGMATVNNCVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKKNMGKQMPQPTFTLRKKLVFPS

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 3 polymer

描述 description	(PHQ)DEVD
分子量 formula_weight	613.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	Q,R,S,T,U,V

XDEVD

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	47

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1f9e.1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.17 — Caspase-like
超家族 Superfamily superfamily	c.17.1 — Caspase-like
家族 Family family	c.17.1.1 — Caspase catalytic domain

结构域编号 domain_id	d1f9e.2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.17 — Caspase-like
超家族 Superfamily superfamily	c.17.1 — Caspase-like
家族 Family family	c.17.1.1 — Caspase catalytic domain

结构域编号 domain_id	d1f9e.3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.17 — Caspase-like
超家族 Superfamily superfamily	c.17.1 — Caspase-like
家族 Family family	c.17.1.1 — Caspase catalytic domain

结构域编号 domain_id	d1f9e.4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.17 — Caspase-like
超家族 Superfamily superfamily	c.17.1 — Caspase-like
家族 Family family	c.17.1.1 — Caspase catalytic domain

结构域编号 domain_id	d1f9e.5
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.17 — Caspase-like
超家族 Superfamily superfamily	c.17.1 — Caspase-like
家族 Family family	c.17.1.1 — Caspase catalytic domain

结构域编号 domain_id	d1f9e.6
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.17 — Caspase-like
超家族 Superfamily superfamily	c.17.1 — Caspase-like
家族 Family family	c.17.1.1 — Caspase catalytic domain

CATH v4.4 (12 domains)

结构域编号 domain_id	1f9eA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1460 —

结构域编号 domain_id	1f9eB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1470 — Caspase-like

结构域编号 domain_id	1f9eC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1460 —

结构域编号 domain_id	1f9eD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1470 — Caspase-like

结构域编号 domain_id	1f9eE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1460 —

结构域编号 domain_id	1f9eF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1470 — Caspase-like

结构域编号 domain_id	1f9eG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1460 —

结构域编号 domain_id	1f9eH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1470 — Caspase-like

结构域编号 domain_id	1f9eI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1460 —

结构域编号 domain_id	1f9eJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1470 — Caspase-like

结构域编号 domain_id	1f9eK00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1460 —

结构域编号 domain_id	1f9eL00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	1470 — Caspase-like

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7. 引用文献 (3)

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晶胞边长 a length_a	98.029 Å
晶胞边长 b length_b	188.748 Å
晶胞边长 c length_c	209.802 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	48

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	19.940 Å
R 因子 r_factor	—
R_work r_work	0.2410
R_free r_free	0.2890

fit	/app/data/saxs_computation/f9/1f9e/1f9e.fit
pddf	/app/data/pr_computation/f9/1f9e/1f9e.pr.out
profile	/app/data/saxs_computation/f9/1f9e/1f9e.dat

CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)