1fq6

X-RAY STRUCTURE OF GLYCOL INHIBITOR PD-133,450 BOUND TO SACCHAROPEPSIN

Method: X-RAY DIFFRACTION D_max: 67.4 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	1fq6
沉积日期 deposition_date	2000-09-03
结构标题 title	X-RAY STRUCTURE OF GLYCOL INHIBITOR PD-133,450 BOUND TO SACCHAROPEPSIN
关键词 keywords	HYDROLASE, 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	20.90 Å
回转半径 Rg (电子) rg_electron	19.93 Å
零角强度 I(0) i0	43741700.00
分子量 molecular_weight	34931.0 kDa
排除体积 excluded_volume	34113 Å³
包络体积 envelope_volume	54452 Å³
水化壳体积 shell_volume	22585 Å³
包络直径 envelope_diameter	68.2 Å
壳层 Rg shell_rg	26.56 Å
包络 Rg envelope_rg	20.05 Å
形状 Rg shape_rg	19.86 Å
总 Rg total_rg	20.68 Å
总原子数 total_atoms	2647
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

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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	67.4 Å
Rg (实空间) rg_real	20.80 Å
Rg 误差 (实空间) rg_real_error	0.30 Å
I(0) (实空间) i0_real	4.3740e+07
I(0) 误差 (实空间) i0_real_error	4.9950e+05
Rg (倒空间) rg_reciprocal	20.82 Å
I(0) (倒空间) i0_reciprocal	43740000.0000
解质量估计 total_estimate	0.8931
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	25.4 Å
偏度 Skewness skewness	0.238
峰度 Kurtosis kurtosis	-0.380
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	8509000.0000
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: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.995

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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	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	2749

GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDIGNNAVGLAKAI

Entity 2 branched

描述 description	;alpha-L-gulopyranose-(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	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	;N-[(1S)-2-{[(2S,3R,4S)-1-cyclohexyl-3,4-dihydroxy-6-methylheptan-2-yl]amino}-1-(ethylsulfanyl)-2-oxoethyl]-Nalpha-(morp holin-4-ylsulfonyl)-L-phenylalaninamide ;
分子量 formula_weight	656.9 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	102

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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	d1fq6a_
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	1fq6A01
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	1fq6A02
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

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7. 引用文献 (2)

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晶胞边长 a length_a	86.910 Å
晶胞边长 b length_b	86.910 Å
晶胞边长 c length_c	110.230 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	2.700 Å
最低分辨率 resolution_low	15.600 Å
R 因子 r_factor	0.1800
R_work r_work	—
R_free r_free	0.2700

fit	/app/data/saxs_computation/fq/1fq6/1fq6.fit
pddf	/app/data/pr_computation/fq/1fq6/1fq6.pr.out
profile	/app/data/saxs_computation/fq/1fq6/1fq6.dat