SAXSdb — 1nju

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nju
沉积日期 deposition_date	2003-01-02
结构标题 title	Complex structure of HCMV Protease and a peptidomimetic inhibitor
关键词 keywords	Protease, Peptidomimetic Inhibitor, Induced-fit, 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	36.36 Å
回转半径 Rg (电子) rg_electron	36.06 Å
零角强度 I(0) i0	336434000.00
分子量 molecular_weight	97420.0 kDa
排除体积 excluded_volume	93264 Å³
包络体积 envelope_volume	168660 Å³
水化壳体积 shell_volume	39804 Å³
包络直径 envelope_diameter	120.4 Å
壳层 Rg shell_rg	41.26 Å
包络 Rg envelope_rg	35.56 Å
形状 Rg shape_rg	36.04 Å
总 Rg total_rg	36.35 Å
总原子数 total_atoms	7392
残基数 n_residues	917
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	120.1 Å
Rg (实空间) rg_real	36.43 Å
Rg 误差 (实空间) rg_real_error	0.96 Å
I(0) (实空间) i0_real	3.3640e+08
I(0) 误差 (实空间) i0_real_error	5.7680e+06
Rg (倒空间) rg_reciprocal	36.39 Å
I(0) (倒空间) i0_reciprocal	336400000.0000
解质量估计 total_estimate	0.8786
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	30.0 Å
偏度 Skewness skewness	0.276
峰度 Kurtosis kurtosis	-0.666
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	108500000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.878; Smooth: 0.890

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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 (2)

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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	d1njua_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.57 — Herpes virus serine proteinase, assemblin
超家族 Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
家族 Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

结构域编号 domain_id	d1njub_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.57 — Herpes virus serine proteinase, assemblin
超家族 Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
家族 Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

结构域编号 domain_id	d1njuc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.57 — Herpes virus serine proteinase, assemblin
超家族 Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
家族 Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

结构域编号 domain_id	d1njud_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.57 — Herpes virus serine proteinase, assemblin
超家族 Superfamily superfamily	b.57.1 — Herpes virus serine proteinase, assemblin
家族 Family family	b.57.1.1 — Herpes virus serine proteinase, assemblin

CATH v4.4 (4 domains)

结构域编号 domain_id	1njuA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

结构域编号 domain_id	1njuB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

结构域编号 domain_id	1njuC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

结构域编号 domain_id	1njuD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	16 — Serine Protease, Human Cytomegalovirus Protease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Herpesvirus/Caudovirus protease domain

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7. 引用文献 (1)

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晶胞边长 a length_a	105.460 Å
晶胞边长 b length_b	213.530 Å
晶胞边长 c length_c	52.330 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	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	25.880 Å
R 因子 r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2730

描述 description	Assemblin
分子量 formula_weight	28130.5 kDa
EC 编号 ec_number	3.4.21.97
突变 mutation	A143Q
来源方法 src_method	man
拷贝数 entity_count	4

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	7392

Complex structure of HCMV Protease and a peptidomimetic inhibitor

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

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Human herpesvirus 5
通用名 common_name	Human cytomegalovirus
NCBI 分类编号 ncbi_taxonomy_id	10359
宿主生物 host_organism	Escherichia coli

描述 description	;N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide ;
分子量 formula_weight	717.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

fit	/app/data/saxs_computation/nj/1nju/1nju.fit
pddf	/app/data/pr_computation/nj/1nju/1nju.pr.out
profile	/app/data/saxs_computation/nj/1nju/1nju.dat