9nir

Human Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (ENPP3) inhibitor complex

Method: X-RAY DIFFRACTION D_max: 129.6 Å Quality: REASONABLE

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	9nir
沉积日期 deposition_date	2025-02-26
最后修订 last_revision	2026-01-07
结构标题 title	Human Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (ENPP3) inhibitor complex
关键词 keywords	EC 3.6.1.9, 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	32.59 Å
回转半径 Rg (电子) rg_electron	32.25 Å
零角强度 I(0) i0	295970000.00
分子量 molecular_weight	91951.0 kDa
排除体积 excluded_volume	88689 Å³
包络体积 envelope_volume	151650 Å³
水化壳体积 shell_volume	40662 Å³
包络直径 envelope_diameter	136.8 Å
壳层 Rg shell_rg	37.39 Å
包络 Rg envelope_rg	32.94 Å
形状 Rg shape_rg	32.13 Å
总 Rg total_rg	32.74 Å
总原子数 total_atoms	6911
残基数 n_residues	814
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	129.6 Å
Rg (实空间) rg_real	32.96 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	2.9600e+08
I(0) 误差 (实空间) i0_real_error	5.2330e+06
Rg (倒空间) rg_reciprocal	32.80 Å
I(0) (倒空间) i0_reciprocal	295900000.0000
解质量估计 total_estimate	0.5893
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	34.4 Å
偏度 Skewness skewness	0.701
峰度 Kurtosis kurtosis	0.414
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	42250000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.445; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.632; Smooth: 0.963

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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 (9)

Entity 1 polymer

描述 description	Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
分子量 formula_weight	94210.9 kDa
EC 编号 ec_number	3.1.4.1,3.6.1.-,3.6.1.9
突变 mutation	Q244K, E275D
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	6963

GSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKFRCGETRLEASLCSCSDDCLQRKDCCADYKSVCQGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLSSKEKNNPAWWHGQPMWLTAMYQGLKAATYFWPGSDVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRIRAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRIDKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLNHLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLDCFCPHLQNSTQLEQVNQMLNLTQEEITATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSPLPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLYPPASNRTSDSQYDALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYDGHFDAPDEITKHLANTDVPIPTHYFVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTNVESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQPVSEILQLKTYLPTF

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	Homo sapiens

Entity 2 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	7

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	{2-[1-(8-methoxyquinazolin-4-yl)piperidin-4-yl]ethyl}phosphonic acid
分子量 formula_weight	351.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 8 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 9 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	52

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7. 引用文献 (1)

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晶胞边长 a length_a	72.932 Å
晶胞边长 b length_b	72.932 Å
晶胞边长 c length_c	382.728 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	8

空间群 space_group	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	30.684 Å
R 因子 r_factor	—
R_work r_work	0.2702
R_free r_free	0.3333

fit	/app/data/saxs_computation/ni/9nir/9nir.fit
pddf	/app/data/pr_computation/ni/9nir/9nir.pr.out
profile	/app/data/saxs_computation/ni/9nir/9nir.dat