1ghy

A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE

Method: X-RAY DIFFRACTION D_max: 60.7 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	1ghy
沉积日期 deposition_date	2001-01-22
结构标题 title	A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE
关键词 keywords	;three-centered, very short hydrogen bond, oxyanion hole water, shift of pKa of His57, structure-based drug design, specificity, urokinase, trypsin, thrombin, Zn+2-mediated inhibition, BLOOD CLOTTING, 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	19.36 Å
回转半径 Rg (电子) rg_electron	18.09 Å
零角强度 I(0) i0	21460500.00
分子量 molecular_weight	34890.0 kDa
排除体积 excluded_volume	43431 Å³
包络体积 envelope_volume	48937 Å³
水化壳体积 shell_volume	21615 Å³
包络直径 envelope_diameter	63.0 Å
壳层 Rg shell_rg	25.33 Å
包络 Rg envelope_rg	18.51 Å
形状 Rg shape_rg	18.07 Å
总 Rg total_rg	19.15 Å
总原子数 total_atoms	4816
残基数 n_residues	296
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	60.7 Å
Rg (实空间) rg_real	19.20 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	2.1460e+07
I(0) 误差 (实空间) i0_real_error	2.5790e+05
Rg (倒空间) rg_reciprocal	19.22 Å
I(0) (倒空间) i0_reciprocal	21460000.0000
解质量估计 total_estimate	0.7990
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	25.6 Å
偏度 Skewness skewness	0.110
峰度 Kurtosis kurtosis	-0.431
角度范围 angular_range	— – 0.4100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9548000.0000
实空间数据点数 n_real_points	72
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 0.978; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; 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 (8)

Entity 1 polymer

描述 description	THROMBIN
分子量 formula_weight	4096.5 kDa
EC 编号 ec_number	3.4.21.5
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L
原子数 atom_count	5966

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

描述 description	THROMBIN
分子量 formula_weight	29594.1 kDa
EC 编号 ec_number	3.4.21.5
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

Entity 3 polymer

描述 description	ACETYL HIRUDIN
分子量 formula_weight	1491.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I

DFEEIPEEYLQ

Entity 4 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	3

Entity 5 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	2-(3-HYDROXY-PYRIDIN-2-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE
分子量 formula_weight	254.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	365

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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	d1ghy.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	1ghyH01
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	1ghyH02
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	71.890 Å
晶胞边长 b length_b	72.220 Å
晶胞边长 c length_c	72.740 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.97 °
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	1.850 Å
最低分辨率 resolution_low	7.000 Å
R 因子 r_factor	0.1960
R_work r_work	0.1950
R_free r_free	0.2200

fit	/app/data/saxs_computation/gh/1ghy/1ghy.fit
pddf	/app/data/pr_computation/gh/1ghy/1ghy.pr.out
profile	/app/data/saxs_computation/gh/1ghy/1ghy.dat

A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE

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 (8)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 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)