SAXSdb — 1fq7

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fq7
沉积日期 deposition_date	2000-09-04
结构标题 title	X-RAY STRUCTURE OF INHIBITOR CP-72,647 BOUND TO SACCHAROPEPSIN
关键词 keywords	Hydrophobic inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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	21.17 Å
回转半径 Rg (电子) rg_electron	19.79 Å
零角强度 I(0) i0	23191900.00
分子量 molecular_weight	37510.0 kDa
排除体积 excluded_volume	47108 Å³
包络体积 envelope_volume	53956 Å³
水化壳体积 shell_volume	22461 Å³
包络直径 envelope_diameter	68.5 Å
壳层 Rg shell_rg	26.54 Å
包络 Rg envelope_rg	19.99 Å
形状 Rg shape_rg	19.76 Å
总 Rg total_rg	20.76 Å
总原子数 total_atoms	2652
残基数 n_residues	329
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	67.3 Å
Rg (实空间) rg_real	21.07 Å
Rg 误差 (实空间) rg_real_error	0.38 Å
I(0) (实空间) i0_real	2.3190e+07
I(0) 误差 (实空间) i0_real_error	2.8560e+05
Rg (倒空间) rg_reciprocal	21.09 Å
I(0) (倒空间) i0_reciprocal	23190000.0000
解质量估计 total_estimate	0.8968
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	26.7 Å
偏度 Skewness skewness	0.213
峰度 Kurtosis kurtosis	-0.397
角度范围 angular_range	— – 0.3750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4705000.0000
实空间数据点数 n_real_points	69
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.976

▶

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

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	SACCHAROPEPSIN
分子量 formula_weight	35774.6 kDa
EC 编号 ec_number	3.4.23.25
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	A
原子数 atom_count	2717

GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDIGNNAVGLAKAI

Entity 2 branched

描述 description	;beta-D-arabino-hexopyranos-2-ulose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	908.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	N-(tert-butoxycarbonyl)-L-phenylalanyl-N-[(2S,3S,5R)-1-cyclohexyl-3-hydroxy-7-methyl-5-(methylcarbamoyl)octan-2-yl]-L-histidinamide
分子量 formula_weight	682.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
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	65

▼

6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1fq7a_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.50 — Acid proteases
超家族 Superfamily superfamily	b.50.1 — Acid proteases
家族 Family family	b.50.1.2 — Pepsin-like

CATH v4.4 (2 domains)

结构域编号 domain_id	1fq7A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1fq7A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	86.430 Å
晶胞边长 b length_b	86.430 Å
晶胞边长 c length_c	109.970 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	28.300 Å
R 因子 r_factor	0.1900
R_work r_work	—
R_free r_free	0.2700

fit	/app/data/saxs_computation/fq/1fq7/1fq7.fit
pddf	/app/data/pr_computation/fq/1fq7/1fq7.pr.out
profile	/app/data/saxs_computation/fq/1fq7/1fq7.dat

X-RAY STRUCTURE OF INHIBITOR CP-72,647 BOUND TO SACCHAROPEPSIN

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