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3hn3

Human beta-glucuronidase at 1.7 A resolution

Method: X-RAY DIFFRACTION Dmax: 135.7 Å Quality: GOOD
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Beta-glucuronidase

Homo sapiens

UniProt P08236

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 × 4 其他聚合物 4 PDB 声明：tetrameric（4） 与蛋白拷贝数一致 链 A； UniProt 21–633 链 B； UniProt 21–633 链 D； UniProt 21–633 链 E； UniProt 21–633 未记录 ;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-L-gulopyranose-(1-2)-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 ; × 1 ;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)-[beta-D-mannopyranose-(1-2)-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 ; × 1 ;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-(1-2)-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 ; × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 BMA beta-D-mannopyranose × 1 X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10mM Tris-HCl pH 7.5, 15% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K 分辨率 1.70 Å R-free 0.240

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 3HN3 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
1BHG HUMAN BETA-GLUCURONIDASE AT 2.6 A RESOLUTION 提交 1996-03-04 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 × 4 PDB 声明：tetrameric
链 A 21–633（613 aa）
链 B 21–633（613 aa）
未记录 未记录非水小分子 X-RAY DIFFRACTION mmCIF 未提供已读取条件 分辨率 2.53 Å R-free 0.310

共 1 个其他 PDB 条目、1 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 BGLR_HUMAN
Isoform —
PDB实体 1
链与序列区间 作者链 A； PDB构建体 1–613； UniProt 21–633 作者链 B； PDB构建体 1–613； UniProt 21–633 作者链 D； PDB构建体 1–613； UniProt 21–633 作者链 E； PDB构建体 1–613； UniProt 21–633

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

SAXS profile for 3hn3

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3hn3
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3hn3
沉积日期 deposition_date2009-05-29
结构标题 titleHuman beta-glucuronidase at 1.7 A resolution
关键词 keywordsLYSOSOMAL ENZYME, ACID HYDROLASE, GLYCOSIDASE, Disease mutation, Glycoprotein, Hydrolase, Lysosome, Mucopolysaccharidosis; HYDROLASE
实验方法 methodX-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_guinier41.76 Å
回转半径 Rg (电子) rg_electron41.16 Å
零角强度 I(0) i01166300000.00
分子量 molecular_weight288810.0 kDa
排除体积 excluded_volume363230 ų
包络体积 envelope_volume447310 ų
水化壳体积 shell_volume85016 ų
包络直径 envelope_diameter141.6 Å
壳层 Rg shell_rg50.37 Å
包络 Rg envelope_rg41.36 Å
形状 Rg shape_rg41.10 Å
总 Rg total_rg41.79 Å
总原子数 total_atoms20430
残基数 n_residues2430
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 Å−1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3
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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax135.7 Å
Rg (实空间) rg_real41.65 Å
Rg 误差 (实空间) rg_real_error0.92 Å
I(0) (实空间) i0_real1.1660e+09
I(0) 误差 (实空间) i0_real_error1.9740e+07
Rg (倒空间) rg_reciprocal41.76 Å
I(0) (倒空间) i0_reciprocal1166000000.0000
解质量估计 total_estimate0.8778
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary50.0 Å
偏度 Skewness skewness0.289
峰度 Kurtosis kurtosis-0.338
角度范围 angular_range— – 0.1900 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha242800000.0000
实空间数据点数 n_real_points39
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.845
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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 (10)

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7. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_idd3hn3a1
类 Class classb — All beta proteins
折叠类型 Fold foldb.18 — Galactose-binding domain-like
超家族 Superfamily superfamilyb.18.1 — Galactose-binding domain-like
家族 Family familyb.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
结构域编号 domain_idd3hn3a2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3hn3a3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.3 — beta-glycanases
结构域编号 domain_idd3hn3b1
类 Class classb — All beta proteins
折叠类型 Fold foldb.18 — Galactose-binding domain-like
超家族 Superfamily superfamilyb.18.1 — Galactose-binding domain-like
家族 Family familyb.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
结构域编号 domain_idd3hn3b2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3hn3b3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.3 — beta-glycanases
结构域编号 domain_idd3hn3d1
类 Class classb — All beta proteins
折叠类型 Fold foldb.18 — Galactose-binding domain-like
超家族 Superfamily superfamilyb.18.1 — Galactose-binding domain-like
家族 Family familyb.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
结构域编号 domain_idd3hn3d2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3hn3d3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.3 — beta-glycanases
结构域编号 domain_idd3hn3e1
类 Class classb — All beta proteins
折叠类型 Fold foldb.18 — Galactose-binding domain-like
超家族 Superfamily superfamilyb.18.1 — Galactose-binding domain-like
家族 Family familyb.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain
结构域编号 domain_idd3hn3e2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family familyb.1.4.1 — beta-Galactosidase/glucuronidase domain
结构域编号 domain_idd3hn3e3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.8 — (Trans)glycosidases
家族 Family familyc.1.8.3 — beta-glycanases

CATH v4.4 (12 domains)

结构域编号 domain_id3hn3A01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily260 — Galactose-binding domain-like
结构域编号 domain_id3hn3A02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3hn3A03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
结构域编号 domain_id3hn3B01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily260 — Galactose-binding domain-like
结构域编号 domain_id3hn3B02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3hn3B03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
结构域编号 domain_id3hn3D01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily260 — Galactose-binding domain-like
结构域编号 domain_id3hn3D02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3hn3D03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
结构域编号 domain_id3hn3E01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily260 — Galactose-binding domain-like
结构域编号 domain_id3hn3E02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins
结构域编号 domain_id3hn3E03
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily80 — Glycosidases
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8. 引用文献 (1)

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9. 文件与曲线 (10)