1xoz

Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Tadalafil

Method: X-RAY DIFFRACTION D_max: 63.9 Å Quality: EXCELLENT

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	1xoz
沉积日期 deposition_date	2004-10-07
结构标题 title	Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Tadalafil
关键词 keywords	Phosphodiesterase, PDE, PDE5A, Tadalafil, Cialis, HYDROLASE; HYDROLASE
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	20.88 Å
回转半径 Rg (电子) rg_electron	19.63 Å
零角强度 I(0) i0	24379900.00
分子量 molecular_weight	38017.0 kDa
排除体积 excluded_volume	47750 Å³
包络体积 envelope_volume	54926 Å³
水化壳体积 shell_volume	22806 Å³
包络直径 envelope_diameter	64.5 Å
壳层 Rg shell_rg	26.77 Å
包络 Rg envelope_rg	20.01 Å
形状 Rg shape_rg	19.63 Å
总 Rg total_rg	20.58 Å
总原子数 total_atoms	2668
残基数 n_residues	325
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	63.9 Å
Rg (实空间) rg_real	20.74 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	2.4380e+07
I(0) 误差 (实空间) i0_real_error	2.9460e+05
Rg (倒空间) rg_reciprocal	20.77 Å
I(0) (倒空间) i0_reciprocal	24380000.0000
解质量估计 total_estimate	0.9033
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.9 Å
偏度 Skewness skewness	0.146
峰度 Kurtosis kurtosis	-0.452
角度范围 angular_range	— – 0.3800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4168000.0000
实空间数据点数 n_real_points	70
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.966

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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 (5)

Entity 1 polymer

描述 description	;cGMP-specific 3',5'-cyclic phosphodiesterase ;
分子量 formula_weight	41827.9 kDa
EC 编号 ec_number	3.1.4.17
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	3020

MGSSHHHHHHSSGLVPRGSHMEEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHPGVSNQFLINTNSELALMYNDESVLEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEKMLINGESGQAKRN

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	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	6-BENZO[1,3]DIOXOL-5-YL-2-METHYL-2,3,6,7,12,12A-HEXAHYDRO-PYRAZINO[1',2':1,6]PYRIDO[3,4-B]INDOLE-1,4-DIONE
分子量 formula_weight	389.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	352

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1xoza_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.211 — HD-domain/PDEase-like
超家族 Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
家族 Family family	a.211.1.2 — PDEase

CATH v4.4 (1 domains)

结构域编号 domain_id	1xozA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
同源超家族 H-superfamily homologous superfamily	10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	56.102 Å
晶胞边长 b length_b	76.397 Å
晶胞边长 c length_c	80.699 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.18 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	1.370 Å
最低分辨率 resolution_low	79.060 Å
R 因子 r_factor	0.1541
R_work r_work	0.1520
R_free r_free	0.1933

fit	/app/data/saxs_computation/xo/1xoz/1xoz.fit
pddf	/app/data/pr_computation/xo/1xoz/1xoz.pr.out
profile	/app/data/saxs_computation/xo/1xoz/1xoz.dat