SAXSdb — 1ju6

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ju6
沉积日期 deposition_date	2001-08-23
结构标题 title	Human Thymidylate Synthase Complex with dUMP and LY231514, A Pyrrolo(2,3-d)pyrimidine-based Antifolate
关键词 keywords	antifolate, dTMP synthesis, drug resistance, cancer, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	45.63 Å
回转半径 Rg (电子) rg_electron	45.64 Å
零角强度 I(0) i0	262160000.00
分子量 molecular_weight	134110.0 kDa
排除体积 excluded_volume	167680 Å³
包络体积 envelope_volume	217330 Å³
水化壳体积 shell_volume	39518 Å³
包络直径 envelope_diameter	145.0 Å
壳层 Rg shell_rg	49.89 Å
包络 Rg envelope_rg	44.70 Å
形状 Rg shape_rg	45.64 Å
总 Rg total_rg	45.80 Å
总原子数 total_atoms	9445
残基数 n_residues	1144
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	137.8 Å
Rg (实空间) rg_real	46.09 Å
Rg 误差 (实空间) rg_real_error	1.11 Å
I(0) (实空间) i0_real	2.6220e+08
I(0) 误差 (实空间) i0_real_error	4.3640e+06
Rg (倒空间) rg_reciprocal	45.63 Å
I(0) (倒空间) i0_reciprocal	262000000.0000
解质量估计 total_estimate	0.6551
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	31.5 Å
偏度 Skewness skewness	0.327
峰度 Kurtosis kurtosis	-1.056
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	79830000.0000
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: 0.343; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.462; Smooth: 0.021

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	THYMIDYLATE SYNTHASE
分子量 formula_weight	35734.9 kDa
EC 编号 ec_number	2.1.1.45
突变 mutation	R46E
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	9493

MPVAGSELPRRPLPPAAQERDAEPRPPHGELQYLGQIQHILRCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV

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	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
分子量 formula_weight	308.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID
分子量 formula_weight	427.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	48

▼

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1ju6a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d1ju6b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d1ju6c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d1ju6d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (4 domains)

结构域编号 domain_id	1ju6A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	1ju6B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	1ju6C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	1ju6D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

▶

7. 引用文献 (2)

▶

晶胞边长 a length_a	68.138 Å
晶胞边长 b length_b	69.633 Å
晶胞边长 c length_c	73.958 Å
晶胞夹角 α angle_alpha	71.67 °
晶胞夹角 β angle_beta	85.72 °
晶胞夹角 γ angle_gamma	75.11 °
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	2.890 Å
最低分辨率 resolution_low	22.950 Å
R 因子 r_factor	0.2390
R_work r_work	0.2360
R_free r_free	0.2640

fit	/app/data/saxs_computation/ju/1ju6/1ju6.fit
pddf	/app/data/pr_computation/ju/1ju6/1ju6.pr.out
profile	/app/data/saxs_computation/ju/1ju6/1ju6.dat

Human Thymidylate Synthase Complex with dUMP and LY231514, A Pyrrolo(2,3-d)pyrimidine-based Antifolate

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution