SAXSdb — 4cia

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

LYSOSOMAL PROTECTIVE PROTEIN

HOMO SAPIENS

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 29–480	未记录	6KZ N-[(2S)-4-methyl-1-oxidanylidene-1-[[(1R,2S)-1-oxidanyl-1-(5-phenyl-1,2,4-oxadiazol-3-yl)butan-2-yl]amino]pentan-2-yl]morpholine-4-carboxamide × 2 CD CADMIUM ION × 14 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATHEPSIN A WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4DEG.C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	分辨率 1.98 Å R-free 0.232

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 4CIA	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1IVY PHYSIOLOGICAL DIMER HPP PRECURSOR 提交 1996-06-12	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 29–480（452 aa）链 B 29–480（452 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 8.3；285 K；PEG 8000, PH 8.0 - 8.3 AT 4 - 12 DEGREES CELSIUS, temperature 285K	分辨率 2.20 Å R-free 0.268
3BP4 The high resolution crystal structure of HLA-B*2705 in complex with a Cathepsin A signal sequence peptide pCatA 提交 2007-12-18	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 2–10（9 aa）片段：Cathepsin A signal sequence, UNP residues 2-10	未记录	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；23% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.85 Å R-free 0.222
3BP7 The high resolution crystal structure of HLA-B*2709 in complex with a Cathepsin A signal sequence peptide, pCatA 提交 2007-12-18	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 2–10（9 aa）片段：Cathepsin A signal sequence, UNP residues 2-10	未记录	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；23.5% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.80 Å R-free 0.204
3BXN The high resolution crystal structure of HLA-B*1402 complexed with a Cathepsin A signal sequence peptide, pCatA 提交 2008-01-14	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 2–10（9 aa）片段：signal sequence peptide, residues 2-10	未记录	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；24- 27%(w/v) PEG 20000, with 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 1.86 Å R-free 0.219
4AZ0 crystal structure of cathepsin a, complexed with 8a. 提交 2012-06-22	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 4 PDB 声明：tetrameric	链 A 29–326（298 aa）链 B 327–480（154 aa）	未记录	S61 (S)-3-{[1-(2-Fluoro-phenyl)-5-hydroxy-1H-pyrazole-3-carbonyl]-amino}-3-o-tolyl-propionic acid × 2 CD CADMIUM ION × 12	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATA WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4 DEG. C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	分辨率 2.17 Å
4AZ3 crystal structure of cathepsin a, complexed with 15a 提交 2012-06-22	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 29–326（298 aa）片段：ACTIVATED PROTEASE RESIDUES 29-326 链 B 327–480（154 aa）片段：ACTIVATED PROTEASE, RESIDUES 327-480	未记录	S35 (3S)-3-({[1-(2-fluorophenyl)-5-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-1H-pyrazol-3-yl]carbonyl}amino)-3-(2-methylphenyl)propanoic acid × 1 CD CADMIUM ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATA WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4 DEG. C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	分辨率 2.04 Å R-free 0.215
4CI9 Crystal structure of cathepsin A, apo-structure 提交 2013-12-06	聚集状态不同配体/离子不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 29–480（452 aa）	未记录	DMS DIMETHYL SULFOXIDE × 2 ACT ACETATE ION × 4 GOL GLYCEROL × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATHEPSIN A WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4DEG.C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	分辨率 1.58 Å R-free 0.191
4CIB crystal structure of cathepsin a, complexed with compound 2 提交 2013-12-06	聚集状态不同配体/离子不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 29–480（452 aa）	未记录	7UZ 2-(cyclohexylmethyl)propanedioic acid × 2 CD CADMIUM ION × 10	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；CATHEPSIN A WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4DEG.C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK.	分辨率 1.89 Å R-free 0.211
4MWS Crystal structure of human PPCA (trigonal crystal form 1) 提交 2013-09-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 29–480（452 aa）链 B 29–480（452 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；10% PEG 3350, 0.1M sodium formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 2.80 Å R-free 0.195
4MWT Crystal structure of human PPCA (trigonal crystal form 2) 提交 2013-09-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 29–480（452 aa）链 B 29–480（452 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；10% PEG 3350, 0.1M ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 3.85 Å R-free 0.325
6WIA CRYSTAL STRUCTURE OF HUMAN PROTECTIVE PROTEIN/CATHEPSIN A, DFP-INHIBITED (AGED) 提交 2020-04-09	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 29–480（452 aa）	非标准单体：是（mmCIF未提供具体位点）	ACT ACETATE ION × 10 CD CADMIUM ION × 12 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；Crystallized in Crystal Screen Cryo II condition #12 (0.095 M cadmium chloride hydrate, 0.095 M sodium acetate trihydrate pH 4.6, 28.5% v/v PEG 400, 5% glycerol). Mounted in 30% glycerol and 70% CS Cryo II condition #12. Protein was inhibited with DFP in 25 mM Tris pH 8, 300 mM NaCl at R.T.	分辨率 2.21 Å R-free 0.224

共 11 个其他 PDB 条目、11 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	PPGB_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 3–454； UniProt 29–480

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	4cia
沉积日期 deposition_date	2013-12-06
结构标题 title	Crystal structure of cathepsin A, complexed with compound 1
关键词 keywords	HYDROLASE, SERINE CARBOXYPEPTIDASE, CARDIOVASCULAR DRUG, HEART FAILURE, ENDOTHELIN, TETRAHEDRAL INTERMEDIATE, COVALENT INHIBITOR; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	22.31 Å
回转半径 Rg (电子) rg_electron	21.11 Å
零角强度 I(0) i0	39622600.00
分子量 molecular_weight	48047.0 kDa
排除体积 excluded_volume	59442 Å³
包络体积 envelope_volume	67683 Å³
水化壳体积 shell_volume	26052 Å³
包络直径 envelope_diameter	75.4 Å
壳层 Rg shell_rg	28.74 Å
包络 Rg envelope_rg	21.44 Å
形状 Rg shape_rg	21.04 Å
总 Rg total_rg	22.19 Å
总原子数 total_atoms	3341
残基数 n_residues	413
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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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	72.5 Å
Rg (实空间) rg_real	22.22 Å
Rg 误差 (实空间) rg_real_error	0.33 Å
I(0) (实空间) i0_real	3.9620e+07
I(0) 误差 (实空间) i0_real_error	4.4280e+05
Rg (倒空间) rg_reciprocal	22.24 Å
I(0) (倒空间) i0_reciprocal	39620000.0000
解质量估计 total_estimate	0.6980
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	28.6 Å
偏度 Skewness skewness	0.276
峰度 Kurtosis kurtosis	-0.237
角度范围 angular_range	— – 0.3550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7606000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 0.189; Positv: 1.000; Valcen: 0.995; Smooth: 0.997

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	LYSOSOMAL PROTECTIVE PROTEIN
分子量 formula_weight	51829.4 kDa
EC 编号 ec_number	3.4.16.5
来源方法 src_method	man
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3710

SRAPDQDEIQRLPGLAKQPSFRQYSGYLKGSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVPSHFRYEKDTVVVQDLGNIFTRLPLKRMWHQALLRSGDKVRMDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPYE

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	SPODOPTERA FRUGIPERDA

实体 2 Entity 2 non-polymer

描述 description	;N-[(2S)-4-methyl-1-oxidanylidene-1-[[(1R,2S)-1-oxidanyl-1-(5-phenyl-1,2,4-oxadiazol-3-yl)butan-2-yl]amino]pentan-2-yl]morpholine-4-carboxamide ;
分子量 formula_weight	459.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 3 Entity 3 non-polymer

描述 description	CADMIUM ION
分子量 formula_weight	112.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

实体 4 Entity 4 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	2

实体 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	358

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7. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d4ciaa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
家族 Family family	c.69.1.5 — Serine carboxypeptidase-like

结构域编号 domain_id	d4ciaa2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d4ciaa3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

结构域编号 domain_id	4ciaA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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8. 引用文献 (2)

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晶胞边长 a length_a	90.106 Å
晶胞边长 b length_b	101.295 Å
晶胞边长 c length_c	48.077 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.91 °
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	—

分辨率 resolution	1.980 Å
最低分辨率 resolution_low	36.110 Å
R 因子 r_factor	0.1729
R_work r_work	0.1699
R_free r_free	0.2320

fit	/app/data/saxs_computation/ci/4cia/4cia.fit
pddf	/app/data/pr_computation/ci/4cia/4cia.pr.out
profile	/app/data/saxs_computation/ci/4cia/4cia.dat

Crystal structure of cathepsin A, complexed with compound 1

1. 蛋白身份与相关结构 Protein Identity & Related Structures

LYSOSOMAL PROTECTIVE PROTEIN

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction