2j0f

Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implication for drug design

Method: X-RAY DIFFRACTION D_max: 136.6 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	2j0f
沉积日期 deposition_date	2006-08-02
结构标题 title	Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implication for drug design
关键词 keywords	;HTP, CHEMOTAXIS, TRANSFERASE, POLYMORPHISM, DISEASE MUTATION, GLYCOSYLTRANSFERASE, ANGIOGENESIS, GROWTH FACTOR, DIFFERENTIATION, DEVELOPMENTAL PROTEIN, HUMAN THYMIDINE PHOSPHORYLASE ;; TRANSFERASE
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	41.88 Å
回转半径 Rg (电子) rg_electron	41.19 Å
零角强度 I(0) i0	520340000.00
分子量 molecular_weight	186260.0 kDa
排除体积 excluded_volume	233320 Å³
包络体积 envelope_volume	302290 Å³
水化壳体积 shell_volume	59702 Å³
包络直径 envelope_diameter	134.2 Å
壳层 Rg shell_rg	48.16 Å
包络 Rg envelope_rg	40.20 Å
形状 Rg shape_rg	41.21 Å
总 Rg total_rg	41.47 Å
总原子数 total_atoms	13063
残基数 n_residues	1784
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	136.6 Å
Rg (实空间) rg_real	41.76 Å
Rg 误差 (实空间) rg_real_error	1.00 Å
I(0) (实空间) i0_real	5.2030e+08
I(0) 误差 (实空间) i0_real_error	9.4750e+06
Rg (倒空间) rg_reciprocal	41.88 Å
I(0) (倒空间) i0_reciprocal	520400000.0000
解质量估计 total_estimate	0.8943
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.122
峰度 Kurtosis kurtosis	-0.626
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	103100000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.930

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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 (3)

Entity 1 polymer

描述 description	THYMIDINE PHOSPHORYLASE
分子量 formula_weight	50030.4 kDa
EC 编号 ec_number	2.4.2.4
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	13513

MAALMTPGTGAPPAPGDFSGEGSQGLPDPSPEPKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGAGAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPLPFAELVLPPQQ

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	THYMINE
分子量 formula_weight	126.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 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	450

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6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

结构域编号 domain_id	2j0fA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	2j0fA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	2j0fA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

结构域编号 domain_id	2j0fB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	2j0fB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	2j0fB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

结构域编号 domain_id	2j0fC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	2j0fC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	2j0fC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

结构域编号 domain_id	2j0fD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	2j0fD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	2j0fD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
同源超家族 H-superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	103.078 Å
晶胞边长 b length_b	76.087 Å
晶胞边长 c length_c	99.575 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.61 °
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	2.310 Å
最低分辨率 resolution_low	102.060 Å
R 因子 r_factor	0.2480
R_work r_work	0.2460
R_free r_free	0.2870

fit	/app/data/saxs_computation/j0/2j0f/2j0f.fit
pddf	/app/data/pr_computation/j0/2j0f/2j0f.pr.out
profile	/app/data/saxs_computation/j0/2j0f/2j0f.dat

Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implication for drug design

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