1pxh

Crystal structure of protein tyrosine phosphatase 1B with potent and selective bidentate inhibitor compound 2

Method: X-RAY DIFFRACTION D_max: 67.0 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	1pxh
沉积日期 deposition_date	2003-07-04
结构标题 title	Crystal structure of protein tyrosine phosphatase 1B with potent and selective bidentate inhibitor compound 2
关键词 keywords	Protein tyrosine phosphatase, PTP1B, Phosphatase inhibitor, HYDROLASE; 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	20.21 Å
回转半径 Rg (电子) rg_electron	19.01 Å
零角强度 I(0) i0	22333200.00
分子量 molecular_weight	35414.0 kDa
排除体积 excluded_volume	44054 Å³
包络体积 envelope_volume	49816 Å³
水化壳体积 shell_volume	21443 Å³
包络直径 envelope_diameter	68.8 Å
壳层 Rg shell_rg	25.92 Å
包络 Rg envelope_rg	19.44 Å
形状 Rg shape_rg	18.99 Å
总 Rg total_rg	19.98 Å
总原子数 total_atoms	2484
残基数 n_residues	297
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	67.0 Å
Rg (实空间) rg_real	20.11 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	2.2330e+07
I(0) 误差 (实空间) i0_real_error	2.3340e+05
Rg (倒空间) rg_reciprocal	20.13 Å
I(0) (倒空间) i0_reciprocal	22330000.0000
解质量估计 total_estimate	0.8787
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	24.9 Å
偏度 Skewness skewness	0.220
峰度 Kurtosis kurtosis	-0.331
角度范围 angular_range	— – 0.3950 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	5153000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.995

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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 (5)

Entity 1 polymer

描述 description	Protein-tyrosine phosphatase, non-receptor type 1
分子量 formula_weight	37365.6 kDa
EC 编号 ec_number	3.1.3.48
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2593

MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN

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 BL21(DE3)

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	;N-{1-[5-(1-CARBAMOYL-2-MERCAPTO-ETHYLCARBAMOYL)-PENTYLCARBAMOYL]-2-[4-(DIFLUORO-PHOSPHONO-METHYL)-PHENYL]-ETHYL}-3-{2-[4-(DIFLUORO-PHOSPHONO-METHYL)-PHENYL]-ACETYLAMINO}-SUCCINAMIC ACID ;
分子量 formula_weight	873.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	109

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1pxha_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
超家族 Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
家族 Family family	c.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases

CATH v4.4 (1 domains)

结构域编号 domain_id	1pxhA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

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7. 引用文献 (1)

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晶胞边长 a length_a	52.840 Å
晶胞边长 b length_b	85.678 Å
晶胞边长 c length_c	88.678 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	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.150 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2030
R_work r_work	0.2000
R_free r_free	0.2070

fit	/app/data/saxs_computation/px/1pxh/1pxh.fit
pddf	/app/data/pr_computation/px/1pxh/1pxh.pr.out
profile	/app/data/saxs_computation/px/1pxh/1pxh.dat