9dpz

Potent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site

Method: X-RAY DIFFRACTION D_max: 93.4 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	9dpz
沉积日期 deposition_date	2024-09-23
最后修订 last_revision	2025-05-28
结构标题 title	Potent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site
关键词 keywords	inhibitor, allosteric, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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	33.31 Å
回转半径 Rg (电子) rg_electron	33.83 Å
零角强度 I(0) i0	127061000.00
分子量 molecular_weight	60837.0 kDa
排除体积 excluded_volume	59210 Å³
包络体积 envelope_volume	106340 Å³
水化壳体积 shell_volume	29308 Å³
包络直径 envelope_diameter	132.2 Å
壳层 Rg shell_rg	35.85 Å
包络 Rg envelope_rg	34.54 Å
形状 Rg shape_rg	33.81 Å
总 Rg total_rg	33.97 Å
总原子数 total_atoms	4600
残基数 n_residues	596
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	93.4 Å
Rg (实空间) rg_real	31.39 Å
Rg 误差 (实空间) rg_real_error	0.31 Å
I(0) (实空间) i0_real	1.2170e+08
I(0) 误差 (实空间) i0_real_error	1.5300e+06
Rg (倒空间) rg_reciprocal	33.75 Å
I(0) (倒空间) i0_reciprocal	127000000.0000
解质量估计 total_estimate	0.6459
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	27.2 Å
偏度 Skewness skewness	0.506
峰度 Kurtosis kurtosis	-0.536
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	1.2210
最高正则化参数 α highest_alpha	14600000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.001; Oscil: 0.874; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.837; Smooth: 0.000

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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 (4)

Entity 1 polymer

描述 description	Protein-arginine deiminase type-4
分子量 formula_weight	74965.9 kDa
EC 编号 ec_number	3.5.3.15
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	4627

GPLGSPEFMAQGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDIAHSPPAKKKSTGSSTWPLDPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAVEISLCADITRTGKVKPTRAVKDQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATRGKLSSKCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHCGTNVRRKPFSFKWWNMVP

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	Insect cell expression vector pTIE1

Entity 2 non-polymer

描述 description	(2S)-2-amino-2-{1-[7-(4-bromophenyl)-5,6-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl]piperidin-4-yl}-1-(pyrrolidin-1-yl)ethan-1-one
分子量 formula_weight	511.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	;[(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone ;
分子量 formula_weight	474.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	27

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7. 引用文献 (1)

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晶胞边长 a length_a	147.339 Å
晶胞边长 b length_b	60.421 Å
晶胞边长 c length_c	113.160 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	123.36 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.410 Å
最低分辨率 resolution_low	47.260 Å
R 因子 r_factor	0.1921
R_work r_work	0.1900
R_free r_free	0.2341

fit	/app/data/saxs_computation/dp/9dpz/9dpz.fit
pddf	/app/data/pr_computation/dp/9dpz/9dpz.pr.out
profile	/app/data/saxs_computation/dp/9dpz/9dpz.dat

Potent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding 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