SAXSdb — 1nnc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nnc
沉积日期 deposition_date	1995-03-15
结构标题 title	INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) COMPLEXED WITH 4-GUANIDINO-NEU5AC2EN INHIBITOR
关键词 keywords	NEURAMINIDASE, SIALIDASE, HYDROLASE (O-GLUCOSYL); HYDROLASE (O-GLUCOSYL)
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	21.23 Å
回转半径 Rg (电子) rg_electron	20.43 Å
零角强度 I(0) i0	37983800.00
分子量 molecular_weight	45679.0 kDa
排除体积 excluded_volume	56161 Å³
包络体积 envelope_volume	64700 Å³
水化壳体积 shell_volume	25397 Å³
包络直径 envelope_diameter	79.0 Å
壳层 Rg shell_rg	28.06 Å
包络 Rg envelope_rg	21.36 Å
形状 Rg shape_rg	20.40 Å
总 Rg total_rg	21.36 Å
总原子数 total_atoms	3202
残基数 n_residues	387
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	77.7 Å
Rg (实空间) rg_real	21.14 Å
Rg 误差 (实空间) rg_real_error	0.51 Å
I(0) (实空间) i0_real	3.7980e+07
I(0) 误差 (实空间) i0_real_error	4.6020e+05
Rg (倒空间) rg_reciprocal	21.16 Å
I(0) (倒空间) i0_reciprocal	37980000.0000
解质量估计 total_estimate	0.8227
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	27.4 Å
偏度 Skewness skewness	0.317
峰度 Kurtosis kurtosis	0.026
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	15290000.0000
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: 0.578; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.982

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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 (7)

Entity 1 polymer

描述 description	NEURAMINIDASE N9
分子量 formula_weight	43723.8 kDa
EC 编号 ec_number	3.2.1.18
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	3399

RDFNNLTKGLCTINSWHIYGKDNAVRIGEDSDVLVTREPYVSCDPDECRFYALSQGTTIRGKHSNGTIHDRSQYRALISWPLSSPPTVYNSRVECIGWSSTSCHDGKTRMSICISGPNNNASAVIWYNRRPVTEINTWARNILRTQESECVCHNGVCPVVFTDGSATGPAETRIYYFKEGKILKWEPLAGTAKHIEECSCYGERAEITCTCRDNWQGSNRPVIRIDPVAMTHTSQYICSPVLTDNPRPNDPTVGKCNDPYPGNNNNGVKGFSYLDGVNTWLGRTISIASRSGYEMLKVPNALTDDKSKPTQGQTIVLNTDWSGYSGSFMDYWAEGECYRACFYVELIRGRPKEDKVWWTSNSIVSMCSSTEFLGQWDWPDGAKIEYFL

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-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	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	alpha-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
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	2

Entity 5 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 6 non-polymer

描述 description	ZANAMIVIR
分子量 formula_weight	332.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	197

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1nnca_
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 (1 domains)

结构域编号 domain_id	1nncA00
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 (7)

Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase.

Protein Sci. (1995)

PMID: 7549872 PRIMARY

Rational Design of Potent Sialidase-Based Inhibitors of Influenza Virus Replication

Nature (1993)

The Structure of the Complex between Influenza Virus Neuraminidase and Sialic Acid, the Viral Receptor

Proteins (1992)

Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants

J.Mol.Biol. (1991)

Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution

J.Mol.Biol. (1991)

The Three-Dimensional Structure of Neuraminidase of Subtype N9 from an Avian Influenza Virus

Proteins (1987)

Structure of the Influenza Virus Glycoprotein Antigen Neuraminidase at 2.9 Angstroms Resolution

Nature (1983)

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晶胞边长 a length_a	182.800 Å
晶胞边长 b length_b	182.800 Å
晶胞边长 c length_c	182.800 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	48

空间群 space_group	I 4 3 2
空间群编号 int_tables_number	211
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.1560
R_work r_work	0.1560
R_free r_free	—

fit	/app/data/saxs_computation/nn/1nnc/1nnc.fit
pddf	/app/data/pr_computation/nn/1nnc/1nnc.pr.out
profile	/app/data/saxs_computation/nn/1nnc/1nnc.dat

INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) COMPLEXED WITH 4-GUANIDINO-NEU5AC2EN INHIBITOR

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution