3iu3

Crystal structure of the Fab fragment of therapeutic antibody Basiliximab in complex with IL-2Ra (CD25) ectodomain

Method: X-RAY DIFFRACTION Dmax: 166.3 Å Quality: GOOD

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

Interleukin-2 receptor alpha chain

Homo sapiens

UniProt P01589

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 异源复合物 蛋白 × 3 其他聚合物 1 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 K; UniProt 22–238 片段:Extracellular domain, ectodomain, UNP residues 22-238 Heavy chain of Fab fragment of Basiliximab × 1 Light chain of Fab fragment of Basiliximab × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2 M KCl, 0.05 M HEPES pH 7.5, and 45% pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.90 Å R-free 0.262
2 其他组合 异源复合物 蛋白 × 3 其他聚合物 1 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 J; UniProt 22–238 片段:Extracellular domain, ectodomain, UNP residues 22-238 Heavy chain of Fab fragment of Basiliximab × 1 Light chain of Fab fragment of Basiliximab × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2 M KCl, 0.05 M HEPES pH 7.5, and 45% pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.90 Å R-free 0.262
3 其他组合 异源复合物 蛋白 × 3 其他聚合物 1 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 I; UniProt 22–238 片段:Extracellular domain, ectodomain, UNP residues 22-238 Heavy chain of Fab fragment of Basiliximab × 1 Light chain of Fab fragment of Basiliximab × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2 M KCl, 0.05 M HEPES pH 7.5, and 45% pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.90 Å R-free 0.262

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。

共 9 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 IL2RA_HUMAN
Isoform
PDB实体 3
链与序列区间 作者链 I; PDB构建体 1–217; UniProt 22–238 作者链 J; PDB构建体 1–217; UniProt 22–238 作者链 K; PDB构建体 1–217; UniProt 22–238

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 3iu3

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3iu3
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3iu3
沉积日期 deposition_date2009-08-29
结构标题 titleCrystal structure of the Fab fragment of therapeutic antibody Basiliximab in complex with IL-2Ra (CD25) ectodomain
关键词 keywords;IL-2Ra, CD25, Basiliximab, Simulect, therapeutic antibody, Disulfide bond, Glycoprotein, Membrane, Receptor, Sushi, Transmembrane, IMMUNE SYSTEM ;; IMMUNE SYSTEM
实验方法 methodX-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier44.64
回转半径 Rg (电子) rg_electron44.52
零角强度 I(0) i0510211000.00
分子量 molecular_weight179090.0 kDa
排除体积 excluded_volume221360 ų
包络体积 envelope_volume324320 ų
水化壳体积 shell_volume62095 ų
包络直径 envelope_diameter180.8
壳层 Rg shell_rg47.37
包络 Rg envelope_rg44.88
形状 Rg shape_rg44.51
总 Rg total_rg44.68
总原子数 total_atoms12566
残基数 n_residues1619
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −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

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

最大尺寸 Dmax dmax166.3
Rg (实空间) rg_real44.79
Rg 误差 (实空间) rg_real_error1.89
I(0) (实空间) i0_real5.1020e+08
I(0) 误差 (实空间) i0_real_error9.3610e+06
Rg (倒空间) rg_reciprocal44.64
I(0) (倒空间) i0_reciprocal510100000.0000
解质量估计 total_estimate0.8422
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary52.3
偏度 Skewness skewness0.441
峰度 Kurtosis kurtosis-0.112
角度范围 angular_range— – 0.1750 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha40650000.0000
实空间数据点数 n_real_points36
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.966

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

6. 实体与聚合物信息 Entities & Polymers (4)

7. 折叠分类 (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

结构域编号 domain_id3iu3A01
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_id3iu3A02
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_id3iu3B01
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_id3iu3B02
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_id3iu3C01
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_id3iu3C02
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_id3iu3D01
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_id3iu3D02
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_id3iu3H01
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_id3iu3H02
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_id3iu3I01
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology70 — Complement Module; domain 1
同源超家族 H-superfamily homologous superfamily10 — Complement Module, domain 1
结构域编号 domain_id3iu3I02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily230
结构域编号 domain_id3iu3J01
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology70 — Complement Module; domain 1
同源超家族 H-superfamily homologous superfamily10 — Complement Module, domain 1
结构域编号 domain_id3iu3J02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily230
结构域编号 domain_id3iu3K01
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology70 — Complement Module; domain 1
同源超家族 H-superfamily homologous superfamily10 — Complement Module, domain 1
结构域编号 domain_id3iu3K02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily230
结构域编号 domain_id3iu3L01
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_id3iu3L02
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

8. 引用文献 (1)

9. 文件与曲线 (10)