9p0v

;Structure of PYCR1 complexed with the allosteric inhibitor 7-benzamido-4-hydroxynaphthalene-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: 118.2 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	9p0v
沉积日期 deposition_date	2025-06-07
结构标题 title	;Structure of PYCR1 complexed with the allosteric inhibitor 7-benzamido-4-hydroxynaphthalene-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	36.96 Å
回转半径 Rg (电子) rg_electron	36.47 Å
零角强度 I(0) i0	653677000.00
分子量 molecular_weight	136140.0 kDa
排除体积 excluded_volume	130180 Å³
包络体积 envelope_volume	234740 Å³
水化壳体积 shell_volume	53425 Å³
包络直径 envelope_diameter	121.1 Å
壳层 Rg shell_rg	42.97 Å
包络 Rg envelope_rg	36.26 Å
形状 Rg shape_rg	36.46 Å
总 Rg total_rg	36.77 Å
总原子数 total_atoms	10256
残基数 n_residues	1387
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	118.2 Å
Rg (实空间) rg_real	36.85 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	6.5370e+08
I(0) 误差 (实空间) i0_real_error	1.0940e+07
Rg (倒空间) rg_reciprocal	36.92 Å
I(0) (倒空间) i0_reciprocal	653700000.0000
解质量估计 total_estimate	0.8929
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	49.5 Å
偏度 Skewness skewness	0.209
峰度 Kurtosis kurtosis	-0.445
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	165600000.0000
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: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.882

▶

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	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	11313

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-benzamido-4-hydroxynaphthalene-2-sulfonic acid
分子量 formula_weight	343.4 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 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	899

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	111.757 Å
晶胞边长 b length_b	180.373 Å
晶胞边长 c length_c	88.206 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.46 °
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	1.800 Å
最低分辨率 resolution_low	42.040 Å
R 因子 r_factor	0.1747
R_work r_work	0.1733
R_free r_free	0.2011

fit	/app/data/saxs_computation/p0/9p0v/9p0v.fit
pddf	/app/data/pr_computation/p0/9p0v/9p0v.pr.out
profile	/app/data/saxs_computation/p0/9p0v/9p0v.dat

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

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