SAXSdb — 1ivd

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ivd
沉积日期 deposition_date	1994-12-12
结构标题 title	STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE
关键词 keywords	HYDROLASE (O-GLYCOSYL); HYDROLASE (O-GLYCOSYL)
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	29.23 Å
回转半径 Rg (电子) rg_electron	28.37 Å
零角强度 I(0) i0	151866000.00
分子量 molecular_weight	91936.0 kDa
排除体积 excluded_volume	112440 Å³
包络体积 envelope_volume	131500 Å³
水化壳体积 shell_volume	38098 Å³
包络直径 envelope_diameter	103.5 Å
壳层 Rg shell_rg	36.22 Å
包络 Rg envelope_rg	28.62 Å
形状 Rg shape_rg	28.34 Å
总 Rg total_rg	29.10 Å
总原子数 total_atoms	8220
残基数 n_residues	776
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	100.2 Å
Rg (实空间) rg_real	29.23 Å
Rg 误差 (实空间) rg_real_error	1.02 Å
I(0) (实空间) i0_real	1.5190e+08
I(0) 误差 (实空间) i0_real_error	2.2290e+06
Rg (倒空间) rg_reciprocal	29.23 Å
I(0) (倒空间) i0_reciprocal	151900000.0000
解质量估计 total_estimate	0.5808
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	31.6 Å
偏度 Skewness skewness	0.366
峰度 Kurtosis kurtosis	-0.372
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	33460000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 0.992; Sysdev: 0.092; Positv: 1.000; Valcen: 0.990; 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	INFLUENZA A SUBTYPE N2 NEURAMINIDASE
分子量 formula_weight	43141.0 kDa
EC 编号 ec_number	3.2.1.18
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	8595

VEYRNWSKPQCQITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPVKCYQFALGQGTTLDNKHSNDTVHDRIPHRTLLMNELGVPFHLGTRQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYDGRLVDSIGSWSQNILRTQESECVCINGTCTVVMTDGSASGRADTRILFIEEGKIVHISPLAGSAQHVEECSCYPRYPGVRCICRDNWKGSNRPVVDINMEDYSIDSSYVCSGLVGDTPRNDDRSSNSNCRDPNNERGTQGVKGWAFDNGNDLWMGRTISKDLRSGYETFKVIGGWSTPNSKSQINRQVIVDSDNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETRVWWTSNSIVVFCGTSGTYGTGSWPDGANINFMPI

来源 Source

来源生物 organism	Influenza A virus (strain A/Tokyo/3/1967 H2N2)
NCBI 分类编号 ncbi_taxonomy_id	380960

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	732.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 5 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	732.7 kDa
来源方法 src_method	man
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	2

Entity 7 non-polymer

描述 description	4-(ACETYLAMINO)-3-HYDROXY-5-NITROBENZOIC ACID
分子量 formula_weight	240.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	125

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ivda_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.1 — Sialidases (neuraminidases)

结构域编号 domain_id	d1ivdb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.1 — Sialidases (neuraminidases)

CATH v4.4 (2 domains)

结构域编号 domain_id	1ivdA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1ivdB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (4)

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晶胞边长 a length_a	120.420 Å
晶胞边长 b length_b	139.830 Å
晶胞边长 c length_c	140.070 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	90.00 °
晶胞分子数 Z z_pdb	16

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	5.000 Å
R 因子 r_factor	0.2250
R_work r_work	0.2250
R_free r_free	—

fit	/app/data/saxs_computation/iv/1ivd/1ivd.fit
pddf	/app/data/pr_computation/iv/1ivd/1ivd.pr.out
profile	/app/data/saxs_computation/iv/1ivd/1ivd.dat

STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution