4gwm

Crystal structure of human promeprin beta

Method: X-RAY DIFFRACTION D_max: 111.1 Å Quality: REASONABLE

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

Meprin A subunit beta

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	其他组合同源多聚体蛋白 × 2 其他聚合物 10 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 23–614 链 B； UniProt 23–614	片段：Promeprin beta ectomoiety, UNP residues 23-614 突变：T23P, P24W	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;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)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ZN ZINC ION × 2 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；18.2%(wt/vol) PEG8000, 1M LiCl, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 1.85 Å R-free 0.188

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 4GWM	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
4GWN Crystal structure of human mature meprin beta 提交 2012-09-03	构建体不同突变/修饰不同配体/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 62–614（553 aa）片段：Mature meprin beta ectomoiety, UNP residues 62-614	未记录	CD CADMIUM ION × 2 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20%(wt/vol) PEG 3350, 0.2M sodium malonate, 0.1M bis-Tris propane, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 3.00 Å R-free 0.238
7AQ1 Crystal structure of human mature meprin beta in complex with the specific inhibitor MWT-S-270 提交 2020-10-20	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：dimer	链 A 62–595（534 aa）链 B 62–595（534 aa）	未记录	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 RUE 3-[[(3-Carboxyphenyl)methyl-[2-(hydroxyamino)-2-oxoethyl]amino]methyl]benzoic acid × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.6；286 K；Protein was mixed with inhibitor in a molar ratio of 1 to 1.2 to a final protein concentration of 8 mg/mL in 30 mM Tris, 100 mM sodium chloride, pH 7.6. 200 nL protein/inhibitor was mixed with 200 nL praezipitation buffer and equilibrated against 55 micro Liter of praezipitation buffer, containing 25 percent (w/v) PEG 4000 and 30 percent (v/v) ethylene glycol.	分辨率 2.41 Å R-free 0.236
7AUW Inhibitory complex of human meprin beta with mouse fetuin-B. 提交 2020-11-03	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 其他组合异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 62–608（547 aa）链 C 62–608（547 aa）	未记录	NA SODIUM ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 9.3；293 K；20.0% PEG smear medium, 0.1M ammonium sulfate, 0.05M magnesium sulfate heptahydrate, 0.1M bicine pH 9.3, 10% ethylene glycol.	分辨率 2.80 Å R-free 0.261

共 3 个其他 PDB 条目、3 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	MEP1B_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–592； UniProt 23–614 作者链 B； PDB构建体 1–592； UniProt 23–614

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。

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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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	4gwm
沉积日期 deposition_date	2012-09-03
结构标题 title	Crystal structure of human promeprin beta
关键词 keywords	Mulidomain structure, Hydrolase; 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	34.27 Å
回转半径 Rg (电子) rg_electron	33.49 Å
零角强度 I(0) i0	304713000.00
分子量 molecular_weight	136190.0 kDa
排除体积 excluded_volume	168320 Å³
包络体积 envelope_volume	219050 Å³
水化壳体积 shell_volume	52817 Å³
包络直径 envelope_diameter	118.2 Å
壳层 Rg shell_rg	41.51 Å
包络 Rg envelope_rg	33.41 Å
形状 Rg shape_rg	33.49 Å
总 Rg total_rg	34.03 Å
总原子数 total_atoms	9572
残基数 n_residues	1115
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	111.1 Å
Rg (实空间) rg_real	34.17 Å
Rg 误差 (实空间) rg_real_error	0.68 Å
I(0) (实空间) i0_real	3.0470e+08
I(0) 误差 (实空间) i0_real_error	4.8000e+06
Rg (倒空间) rg_reciprocal	34.23 Å
I(0) (倒空间) i0_reciprocal	304700000.0000
解质量估计 total_estimate	0.6568
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	43.5 Å
偏度 Skewness skewness	0.285
峰度 Kurtosis kurtosis	-0.274
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	48370000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.921

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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 (14)

实体 1 Entity 1 polymer

描述 description	Meprin A subunit beta
分子量 formula_weight	67286.7 kDa
EC 编号 ec_number	3.4.24.63
突变 mutation	T23P, P24W
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	10380

PWENFDVDGGMDQDIFDINEGLGLDLFEGDIRLDRAQIRNSIIGEKYRWPHTIPYVLEDSLEMNAKGVILNAFERYRLKTCIDFKPWAGETNYISVFKGSGCWSSVGNRRVGKQELSIGANCDRIATVQHEFLHALGFWHEQSRSDRDDYVRIMWDRILSGREHNFNTYSDDISDSLNVPYDYTSVMHYSKTAFQNGTEPTIVTRISDFEDVIGQRMDFSDSDLLKLNQLYNCSSSLSFMDSCSFELENVCGMIQSSGDNADWQRVSQVPRGPESDHSNMGQCQGSGFFMHFDSSSVNVGATAVLESRTLYPKRGFQCLQFYLYNSGSESDQLNIYIREYSADNVDGNLTLVEEIKEIPTGSWQLYHVTLKVTKKFRVVFEGRKGSGASLGGLSIDDINLSETRCPHHIWHIRNFTQFIGSPNGTLYSPPFYSSKGYAFQIYLNLAHVTNAGIYFHLISGANDDQLQWPCPWQQATMTLLDQNPDIRQRMSNQRSITTDPFMTTDNGNYFWDRPSKVGTVALFSNGTQFRRGGGYGTSAFITHERLKSRDFIKGDDVYILLTVEDISHLNSTQIQLTPAPSVQDLCSKTTCK

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	Trichoplusia ni

实体 2 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	2

实体 3 Entity 3 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)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1203.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 4 Entity 4 branched

描述 description	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	367.3 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-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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	1559.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 6 Entity 6 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

实体 7 Entity 7 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)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1041.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 8 Entity 8 branched

描述 description	;alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	716.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 9 Entity 9 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

实体 10 Entity 10 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 11 Entity 11 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 12 Entity 12 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	5

实体 13 Entity 13 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 14 Entity 14 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	808

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7. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id	4gwmA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	4gwmA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	4gwmA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

结构域编号 domain_id	4gwmB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	4gwmB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	4gwmB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

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8. 引用文献 (1)

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晶胞边长 a length_a	69.620 Å
晶胞边长 b length_b	71.120 Å
晶胞边长 c length_c	85.740 Å
晶胞夹角 α angle_alpha	74.87 °
晶胞夹角 β angle_beta	80.08 °
晶胞夹角 γ angle_gamma	65.13 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	1.850 Å
最低分辨率 resolution_low	48.450 Å
R 因子 r_factor	0.1684
R_work r_work	0.1682
R_free r_free	0.1879

fit	/app/data/saxs_computation/gw/4gwm/4gwm.fit
pddf	/app/data/pr_computation/gw/4gwm/4gwm.pr.out
profile	/app/data/saxs_computation/gw/4gwm/4gwm.dat