1kbo

;Complex of Human recombinant NAD(P)H:Quinone Oxide reductase type 1 with 5-methoxy-1,2-dimethyl-3-(phenoxymethyl)indole-4,7-dione (ES1340) ;

Method: X-RAY DIFFRACTION D_max: 141.8 Å Quality: REASONABLE

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	1kbo
沉积日期 deposition_date	2001-11-06
结构标题 title	;Complex of Human recombinant NAD(P)H:Quinone Oxide reductase type 1 with 5-methoxy-1,2-dimethyl-3-(phenoxymethyl)indole-4,7-dione (ES1340) ;
关键词 keywords	FLAVOENZYME, PRODRUG-ENZYME COMPLEX, OXIDOREDUCTASE; OXIDOREDUCTASE
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	44.96 Å
回转半径 Rg (电子) rg_electron	44.99 Å
零角强度 I(0) i0	218216000.00
分子量 molecular_weight	127350.0 kDa
排除体积 excluded_volume	161210 Å³
包络体积 envelope_volume	208070 Å³
水化壳体积 shell_volume	38048 Å³
包络直径 envelope_diameter	146.5 Å
壳层 Rg shell_rg	50.57 Å
包络 Rg envelope_rg	43.76 Å
形状 Rg shape_rg	44.97 Å
总 Rg total_rg	45.31 Å
总原子数 total_atoms	9004
残基数 n_residues	1092
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	141.8 Å
Rg (实空间) rg_real	45.37 Å
Rg 误差 (实空间) rg_real_error	1.49 Å
I(0) (实空间) i0_real	2.1820e+08
I(0) 误差 (实空间) i0_real_error	4.2880e+06
Rg (倒空间) rg_reciprocal	44.97 Å
I(0) (倒空间) i0_reciprocal	218100000.0000
解质量估计 total_estimate	0.6395
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.4 Å
偏度 Skewness skewness	0.303
峰度 Kurtosis kurtosis	-1.079
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	106300000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.190; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.454; Smooth: 0.287

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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 (4)

Entity 1 polymer

描述 description	NAD(P)H dehydrogenase [quinone] 1
分子量 formula_weight	30776.4 kDa
EC 编号 ec_number	1.6.99.2
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	9169

VGRRALIVLAHSERTSFNYAMKEAAAAALKKKGWEVVESDLYAMNFNPIISRKDITGKLKDPANFQYPAESVLAYKEGHLSPDIVAEQKKLEAADLVIFQFPLQWFGVPAILKGWFERVFIGEFAYTYAAMYDKGPFRSKKAVLSITTGGSGSMYSLQGIHGDMNVILWPIQSGILHFCGFQVLEPQLTYSIGHTPADARIQILEGWKKRLENIWDETPLYFAPSSLFDLNFQAGFLMKKEVQDEEKNKKFGLSVGHHLGKSIPTDNQIKARK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	5-METHOXY-1,2-DIMETHYL-3-(PHENOXYMETHYL)INDOLE-4,7-DIONE
分子量 formula_weight	311.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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	165

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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	d1kboa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.5 — Flavoproteins
家族 Family family	c.23.5.3 — Quinone reductase

结构域编号 domain_id	d1kbob_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.5 — Flavoproteins
家族 Family family	c.23.5.3 — Quinone reductase

结构域编号 domain_id	d1kboc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.5 — Flavoproteins
家族 Family family	c.23.5.3 — Quinone reductase

结构域编号 domain_id	d1kbod_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.23 — Flavodoxin-like
超家族 Superfamily superfamily	c.23.5 — Flavoproteins
家族 Family family	c.23.5.3 — Quinone reductase

CATH v4.4 (4 domains)

结构域编号 domain_id	1kboA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	360 — Flavodoxin domain

结构域编号 domain_id	1kboB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	360 — Flavodoxin domain

结构域编号 domain_id	1kboC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	360 — Flavodoxin domain

结构域编号 domain_id	1kboD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	360 — Flavodoxin domain

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7. 引用文献 (3)

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晶胞边长 a length_a	55.636 Å
晶胞边长 b length_b	57.026 Å
晶胞边长 c length_c	96.878 Å
晶胞夹角 α angle_alpha	76.80 °
晶胞夹角 β angle_beta	76.93 °
晶胞夹角 γ angle_gamma	86.28 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	35.550 Å
R 因子 r_factor	0.2071
R_work r_work	0.2000
R_free r_free	0.2870

fit	/app/data/saxs_computation/kb/1kbo/1kbo.fit
pddf	/app/data/pr_computation/kb/1kbo/1kbo.pr.out
profile	/app/data/saxs_computation/kb/1kbo/1kbo.dat