2cml

Structure of Neuraminidase from English Duck Subtype N6 Complexed with 30 MM ZANAMIVIR, Crystal Soaked for 3 Hours at 291 K.

Method: X-RAY DIFFRACTION D_max: 112.3 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	2cml
沉积日期 deposition_date	2006-05-10
结构标题 title	Structure of Neuraminidase from English Duck Subtype N6 Complexed with 30 MM ZANAMIVIR, Crystal Soaked for 3 Hours at 291 K.
关键词 keywords	HB SITE, HYDROLASE, SUBTYPE N6, GLYCOSIDASE, INFLUENZA TYPE A, SIALIC ACID, NEURAMINIDASE, TRANSMEMBRANE; HYDROLASE
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	35.32 Å
回转半径 Rg (电子) rg_electron	34.57 Å
零角强度 I(0) i0	544839000.00
分子量 molecular_weight	181280.0 kDa
排除体积 excluded_volume	223060 Å³
包络体积 envelope_volume	262990 Å³
水化壳体积 shell_volume	60011 Å³
包络直径 envelope_diameter	117.0 Å
壳层 Rg shell_rg	43.61 Å
包络 Rg envelope_rg	34.47 Å
形状 Rg shape_rg	34.54 Å
总 Rg total_rg	35.22 Å
总原子数 total_atoms	12674
残基数 n_residues	1556
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	112.3 Å
Rg (实空间) rg_real	35.17 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	5.4480e+08
I(0) 误差 (实空间) i0_real_error	8.3800e+06
Rg (倒空间) rg_reciprocal	35.27 Å
I(0) (倒空间) i0_reciprocal	544900000.0000
解质量估计 total_estimate	0.8973
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	109.8 Å
偏度 Skewness skewness	0.170
峰度 Kurtosis kurtosis	-0.521
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	272900000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.929

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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 (10)

Entity 1 polymer

描述 description	NEURAMINIDASE
分子量 formula_weight	43011.5 kDa
EC 编号 ec_number	3.2.1.18
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	13060

RTFLNLTKPLCEVNSWHILSKDNAIRIGEDAHILVTREPYLSCDPQGCRMFALSQGTTLRGRHANGTIHDRSPFRALISWEMGQAPSPYNTRVECIGWSSTSCHDGMSRMSICMSGPNNNASAVVWYGGRPITEIPSWAGNILRTQESECVCHKGVCPVVMTDGPANNRAATKIIYFKEGKIQKIEELAGNAQHIEECSCYGAGGVIKCICRDNWKGANRPVITIDPEMMTHTSKYLCSKVLTDTSRPNDPTNGNCDAPITGGSPDPGVKGFAFLDGENSWLGRTISKDSRSGYEMLKVPNAETDIQSGPISNQVIVNNQNWSGYSGAFIDYWANKECFNPCFYVELIRGRPKESSVLWTSNSIVALCGSKKRLGSWSWHDGAEIIYFE

来源 Source

来源生物 organism	INFLUENZA A VIRUS
NCBI 分类编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	GALLUS GALLUS

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	3

Entity 3 branched

描述 description	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose
分子量 formula_weight	504.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-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 5 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	8

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	4

Entity 7 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	11

Entity 8 non-polymer

描述 description	beta-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 9 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	8

Entity 10 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	386

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2cmla_
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	d2cmlb_
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	d2cmlc_
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	d2cmld_
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 (4 domains)

结构域编号 domain_id	2cmlA00
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	2cmlB00
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	2cmlC00
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	2cmlD00
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 (1)

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晶胞边长 a length_a	106.241 Å
晶胞边长 b length_b	73.685 Å
晶胞边长 c length_c	106.684 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.29 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	30.700 Å
R 因子 r_factor	0.1830
R_work r_work	0.1800
R_free r_free	0.2320

fit	/app/data/saxs_computation/cm/2cml/2cml.fit
pddf	/app/data/pr_computation/cm/2cml/2cml.pr.out
profile	/app/data/saxs_computation/cm/2cml/2cml.dat