SAXSdb — 1b5f

▼

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

当前条目没有可用的 UniProt 蛋白身份。

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白链接。

当前条目的 assembly 组成

Assembly	聚集状态	实体与构建体证据	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	其他组合异源复合物蛋白 4 / DNA 0 / RNA 0 / 其他聚合物 4 PDB 声明：tetrameric	实体 1：PROTEIN (CARDOSIN A) × 2 实体 2：PROTEIN (CARDOSIN A) × 2 实体 3：;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 实体 4：;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 实体 5：;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 缺少 UniProt 身份时不显示参考序列区间	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件：pH 5.5；LYOPHILIZED PROTEIN DISSOLVED IN WATER TO 12 MG/ML, SITTING DROPS OF PROTEIN SOLUTION AN ALIQUOTA OF PRECIPITANT SOLUTION, COMPOSED OF PEG 4 K 40%, SODIUM CITRATE BUFFER 0.1 M AND AMMONIUM ACETATE 0.2 M, pH 5.5	分辨率 1.72 Å R-free 0.256
2	其他组合异源复合物蛋白 2 / DNA 0 / RNA 0 / 其他聚合物 2 PDB 声明：dimeric	实体 1：PROTEIN (CARDOSIN A) × 1 实体 2：PROTEIN (CARDOSIN A) × 1 实体 3：;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 实体 4：;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 缺少 UniProt 身份时不显示参考序列区间	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件：pH 5.5；LYOPHILIZED PROTEIN DISSOLVED IN WATER TO 12 MG/ML, SITTING DROPS OF PROTEIN SOLUTION AN ALIQUOTA OF PRECIPITANT SOLUTION, COMPOSED OF PEG 4 K 40%, SODIUM CITRATE BUFFER 0.1 M AND AMMONIUM ACETATE 0.2 M, pH 5.5	分辨率 1.72 Å R-free 0.256
3	其他组合异源复合物蛋白 2 / DNA 0 / RNA 0 / 其他聚合物 2 PDB 声明：dimeric	实体 1：PROTEIN (CARDOSIN A) × 1 实体 2：PROTEIN (CARDOSIN A) × 1 实体 4：;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 实体 5：;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 缺少 UniProt 身份时不显示参考序列区间	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件：pH 5.5；LYOPHILIZED PROTEIN DISSOLVED IN WATER TO 12 MG/ML, SITTING DROPS OF PROTEIN SOLUTION AN ALIQUOTA OF PRECIPITANT SOLUTION, COMPOSED OF PEG 4 K 40%, SODIUM CITRATE BUFFER 0.1 M AND AMMONIUM ACETATE 0.2 M, pH 5.5	分辨率 1.72 Å R-free 0.256

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。

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id	1b5f
沉积日期 deposition_date	1999-01-06
结构标题 title	NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.
关键词 keywords	HYDROLASE, ASPARTIC PROTEINASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	28.98 Å
回转半径 Rg (电子) rg_electron	28.42 Å
零角强度 I(0) i0	87581100.00
分子量 molecular_weight	74193.0 kDa
排除体积 excluded_volume	92814 Å³
包络体积 envelope_volume	114300 Å³
水化壳体积 shell_volume	34004 Å³
包络直径 envelope_diameter	100.3 Å
壳层 Rg shell_rg	35.19 Å
包络 Rg envelope_rg	28.38 Å
形状 Rg shape_rg	28.37 Å
总 Rg total_rg	29.23 Å
总原子数 total_atoms	5229
残基数 n_residues	651
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

▼

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

最大尺寸 Dmax dmax	96.0 Å
Rg (实空间) rg_real	29.04 Å
Rg 误差 (实空间) rg_real_error	0.73 Å
I(0) (实空间) i0_real	8.7580e+07
I(0) 误差 (实空间) i0_real_error	1.3250e+06
Rg (倒空间) rg_reciprocal	29.02 Å
I(0) (倒空间) i0_reciprocal	87580000.0000
解质量估计 total_estimate	0.8730
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.462
峰度 Kurtosis kurtosis	-0.153
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15870000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.836

▶

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

▶

6. 实体与聚合物信息 Entities & Polymers (6)

实体 1 Entity 1 polymer

描述 description	PROTEIN (CARDOSIN A)
分子量 formula_weight	26042.8 kDa
EC 编号 ec_number	3.4.23.-
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	5842

GSAVVALTNDRDTSYFGEIGIGTPPQKFTVIFDTGSSVLWVPSSKCINSKACRAHSMYESSDSSTYKENGTFGAIIYGTGSITGFFSQDSVTIGDLVVKEQDFIEATDEADNVFLHRLFDGILGLSFQTISVPVWYNMLNQGLVKERRFSFWLNRNVDEEEGGELVFGGLDPNHFRGDHTYVPVTYQYYWQFGIGDVLIGDKSTGFCAPGCQAFADSGTSLLSGPTAIVTQINHAIGAN

实体 2 Entity 2 polymer

描述 description	PROTEIN (CARDOSIN A)
分子量 formula_weight	9441.8 kDa
EC 编号 ec_number	3.4.23.-
来源方法 src_method	nat
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	B,D

EELQVDCNTLSSMPNVSFTIGGKKFGLTPEQYILKVGKGEATQCISGFTAMDATLLGPLWILGDVFMRPYHTVFDYGNLLVGFAEAA

实体 3 Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	894.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 4 Entity 4 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	732.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 5 Entity 5 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1057.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 6 Entity 6 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	528

▼

7. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1b5f.1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.50 — Acid proteases
超家族 Superfamily superfamily	b.50.1 — Acid proteases
家族 Family family	b.50.1.2 — Pepsin-like

结构域编号 domain_id	d1b5f.2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.50 — Acid proteases
超家族 Superfamily superfamily	b.50.1 — Acid proteases
家族 Family family	b.50.1.2 — Pepsin-like

CATH v4.4 (4 domains)

结构域编号 domain_id	1b5fA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1b5fB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1b5fC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

结构域编号 domain_id	1b5fD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	70 — Cathepsin D, subunit A; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Acid Proteases

▶

8. 引用文献 (3)

▶

晶胞边长 a length_a	116.964 Å
晶胞边长 b length_b	87.186 Å
晶胞边长 c length_c	81.303 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	104.43 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	1.720 Å
最低分辨率 resolution_low	34.800 Å
R 因子 r_factor	0.2050
R_work r_work	—
R_free r_free	0.2560

fit	/app/data/saxs_computation/b5/1b5f/1b5f.fit
pddf	/app/data/pr_computation/b5/1b5f/1b5f.pr.out
profile	/app/data/saxs_computation/b5/1b5f/1b5f.dat

NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.

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

当前条目的 assembly 组成

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

6. 实体与聚合物信息 Entities & Polymers (6)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 branched

实体 4 Entity 4 branched

实体 5 Entity 5 branched

实体 6 Entity 6 water

7. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. 引用文献 (3)

9. 文件与曲线 (10)

Files (7)

Curves (3)