9p0t

;Structure of PYCR1 complexed with the allosteric inhibitor 4-hydroxy-7-(phenylamino)naphthalene-2-sulfonic acid in a remote site and NADH and (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid in the active site ;

Method: X-RAY DIFFRACTION D_max: 117.5 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9p0t
沉积日期 deposition_date	2025-06-07
结构标题 title	;Structure of PYCR1 complexed with the allosteric inhibitor 4-hydroxy-7-(phenylamino)naphthalene-2-sulfonic acid in a remote site and NADH and (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid in the active site ;
关键词 keywords	AMINO-ACID BIOSYNTHESIS, OXIDOREDUCTASE, PROLINE BIOSYNTHESIS, INHIBITOR, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
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	36.89 Å
回转半径 Rg (电子) rg_electron	36.40 Å
零角强度 I(0) i0	653085000.00
分子量 molecular_weight	136140.0 kDa
排除体积 excluded_volume	130240 Å³
包络体积 envelope_volume	233840 Å³
水化壳体积 shell_volume	53274 Å³
包络直径 envelope_diameter	121.1 Å
壳层 Rg shell_rg	42.89 Å
包络 Rg envelope_rg	36.24 Å
形状 Rg shape_rg	36.39 Å
总 Rg total_rg	36.71 Å
总原子数 total_atoms	10258
残基数 n_residues	1377
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	117.5 Å
Rg (实空间) rg_real	36.78 Å
Rg 误差 (实空间) rg_real_error	0.80 Å
I(0) (实空间) i0_real	6.5310e+08
I(0) 误差 (实空间) i0_real_error	1.0210e+07
Rg (倒空间) rg_reciprocal	36.85 Å
I(0) (倒空间) i0_reciprocal	653100000.0000
解质量估计 total_estimate	0.8928
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	49.2 Å
偏度 Skewness skewness	0.209
峰度 Kurtosis kurtosis	-0.448
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	168400000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.867

▶

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

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	Pyrroline-5-carboxylate reductase 1, mitochondrial
分子量 formula_weight	33532.6 kDa
EC 编号 ec_number	1.5.1.2
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E
原子数 atom_count	11285

MHHHHHHSSGVDLGTENLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQEQVSPAAIKKTILDKVKLDS

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	(2S)-2-hydroxy-3,3-dimethylbutanoic acid
分子量 formula_weight	132.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 3 non-polymer

描述 description	7-anilino-4-hydroxynaphthalene-2-sulfonic acid
分子量 formula_weight	315.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 4 non-polymer

描述 description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
分子量 formula_weight	665.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 5 non-polymer

描述 description	DI(HYDROXYETHYL)ETHER
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	894

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	112.540 Å
晶胞边长 b length_b	180.592 Å
晶胞边长 c length_c	88.109 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.62 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	20

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	1.790 Å
最低分辨率 resolution_low	47.710 Å
R 因子 r_factor	0.1968
R_work r_work	0.1954
R_free r_free	0.2230

fit	/app/data/saxs_computation/p0/9p0t/9p0t.fit
pddf	/app/data/pr_computation/p0/9p0t/9p0t.pr.out
profile	/app/data/saxs_computation/p0/9p0t/9p0t.dat