1gj8

ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS

Method: X-RAY DIFFRACTION D_max: 60.2 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	1gj8
沉积日期 deposition_date	2001-04-27
结构标题 title	ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS
关键词 keywords	selectivity at S1, H2O displacement, uPA, tPA, Ser190/Ala190 protease, structure-based drug design, BLOOD CLOTTING, hydrolase; BLOOD CLOTTING, 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	18.65 Å
回转半径 Rg (电子) rg_electron	17.48 Å
零角强度 I(0) i0	16243900.00
分子量 molecular_weight	29745.0 kDa
排除体积 excluded_volume	36916 Å³
包络体积 envelope_volume	41056 Å³
水化壳体积 shell_volume	19180 Å³
包络直径 envelope_diameter	60.7 Å
壳层 Rg shell_rg	24.30 Å
包络 Rg envelope_rg	17.87 Å
形状 Rg shape_rg	17.47 Å
总 Rg total_rg	18.49 Å
总原子数 total_atoms	4103
残基数 n_residues	258
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	60.2 Å
Rg (实空间) rg_real	18.53 Å
Rg 误差 (实空间) rg_real_error	0.24 Å
I(0) (实空间) i0_real	1.6240e+07
I(0) 误差 (实空间) i0_real_error	1.8840e+05
Rg (倒空间) rg_reciprocal	18.55 Å
I(0) (倒空间) i0_reciprocal	16240000.0000
解质量估计 total_estimate	0.8852
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	23.9 Å
偏度 Skewness skewness	0.178
峰度 Kurtosis kurtosis	-0.344
角度范围 angular_range	— – 0.4250 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	4620000.0000
实空间数据点数 n_real_points	74
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 1.000

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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 (5)

Entity 1 polymer

描述 description	UROKINASE-TYPE PLASMINOGEN ACTIVATOR
分子量 formula_weight	2708.2 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	4848

KPSSPPEELKFQCGQKTLRPRFK

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	UROKINASE-TYPE PLASMINOGEN ACTIVATOR
分子量 formula_weight	28435.4 kDa
EC 编号 ec_number	3.4.21.73
突变 mutation	N145A
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	B

IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLMSPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICLPSMYNDPQFGTSCEITGFGKEASTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL

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 non-polymer

描述 description	CITRIC ACID
分子量 formula_weight	192.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	6-FLUORO-2-(2-HYDROXY-3-ISOBUTOXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE
分子量 formula_weight	342.4 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	227

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1gj8.1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.47 — Trypsin-like serine proteases
超家族 Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
家族 Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (2 domains)

结构域编号 domain_id	1gj8B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	1gj8B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

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7. 引用文献 (1)

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晶胞边长 a length_a	81.770 Å
晶胞边长 b length_b	50.020 Å
晶胞边长 c length_c	66.940 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	113.76 °
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	1.640 Å
最低分辨率 resolution_low	7.000 Å
R 因子 r_factor	0.1900
R_work r_work	0.1880
R_free r_free	0.2210

fit	/app/data/saxs_computation/gj/1gj8/1gj8.fit
pddf	/app/data/pr_computation/gj/1gj8/1gj8.pr.out
profile	/app/data/saxs_computation/gj/1gj8/1gj8.dat

ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS

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 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)