9hjg

;Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex with an N6-disubstituted acyclic ADP analog (compound 26 in publication) in the closed state ;

Method: X-RAY DIFFRACTION D_max: 159.5 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9hjg
沉积日期 deposition_date	2024-11-29
最后修订 last_revision	2025-05-28
结构标题 title	;Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex with an N6-disubstituted acyclic ADP analog (compound 26 in publication) in the closed state ;
关键词 keywords	nucleotide analog, dimetal center, closed state, 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	44.81 Å
回转半径 Rg (电子) rg_electron	45.06 Å
零角强度 I(0) i0	781140000.00
分子量 molecular_weight	233620.0 kDa
排除体积 excluded_volume	293170 Å³
包络体积 envelope_volume	369110 Å³
水化壳体积 shell_volume	68588 Å³
包络直径 envelope_diameter	173.1 Å
壳层 Rg shell_rg	49.03 Å
包络 Rg envelope_rg	44.63 Å
形状 Rg shape_rg	45.23 Å
总 Rg total_rg	44.66 Å
总原子数 total_atoms	32689
残基数 n_residues	2083
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	159.5 Å
Rg (实空间) rg_real	44.91 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	7.8110e+08
I(0) 误差 (实空间) i0_real_error	1.5190e+07
Rg (倒空间) rg_reciprocal	44.81 Å
I(0) (倒空间) i0_reciprocal	781000000.0000
解质量估计 total_estimate	0.8611
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	54.7 Å
偏度 Skewness skewness	0.402
峰度 Kurtosis kurtosis	-0.215
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	162400000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.926

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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	5'-nucleotidase
分子量 formula_weight	60405.4 kDa
EC 编号 ec_number	3.1.3.35,3.1.3.5,3.1.3.89,3.1.3.91,3.1.3.99
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	32727

WELTILHTNDVHSRLEQTSEDSSKCVDASRCMGGVARLFTKVQQIRRAEPNVLLLDAGDQYQGTIWFTVYKGAEVAHFMNALRYDAMALGNHEFDNGVEGLIEPLLKEAKFPILSANIKAKGPLASQISGLYLPYKVLPVGDEVVGIVGYTSKETPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEMDKLIAQKVRGVDVVVGGHSNTFLYTGNPPSKEVPAGKYPFIVTSDDGRKVPVVQAYAFGKYLGYLKIEFDERGNVISSHGNPILLDSSIPEDPSIKADINKWRIKLDDYSTQELGKTIVYLDGSSQSCRFRECNMGNLICDAMINNNLRHTDEMFWNHVSMCILNGGGIRSPIDERNDGTITWENLAAVLPFGGTFDLVQLKGSTLKKAFEHSVHRYGQSTGEFLQVGGIHVVYDLSRKPGDRVVKLDVLCTKCRVPSYDPLKMDEVYKVILPNFLANGGDGFQMIKDELLRHDSGDQDINVVSTYISKMKVIYPAVEGRIKFSGGGGAGGGGGTDDDDKWSHPQFEK

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 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	8

Entity 3 non-polymer

描述 description	[5-[2-chloranyl-6-[methyl-(phenylmethyl)amino]purin-9-yl]pentoxy-oxidanyl-phosphoryl]methylphosphonic acid
分子量 formula_weight	517.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 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 5 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

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7. 引用文献 (1)

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晶胞边长 a length_a	93.593 Å
晶胞边长 b length_b	84.551 Å
晶胞边长 c length_c	124.667 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	102.62 °
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	121.660 Å
R 因子 r_factor	0.2385
R_work r_work	0.2368
R_free r_free	0.2711

fit	/app/data/saxs_computation/hj/9hjg/9hjg.fit
pddf	/app/data/pr_computation/hj/9hjg/9hjg.pr.out
profile	/app/data/saxs_computation/hj/9hjg/9hjg.dat

;Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex with an N6-disubstituted acyclic ADP analog (compound 26 in publication) in the closed state ;

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