3nfp

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

Method: X-RAY DIFFRACTION Dmax: 154.8 Å Quality: GOOD

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

Interleukin-2 receptor subunit alpha

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 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 K; UniProt 22–238 片段:UNP residues 22-238 Heavy chain of Fab fragment of daclizumab × 1 Light chain of Fab fragment of daclizumab × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.86 Å R-free 0.301
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 I; UniProt 22–238 片段:UNP residues 22-238 Heavy chain of Fab fragment of daclizumab × 1 Light chain of Fab fragment of daclizumab × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.86 Å R-free 0.301

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、12 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 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 3nfp

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id3nfp
沉积日期 deposition_date2010-06-10
结构标题 titleCrystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain
关键词 keywordsIL-2Ra, CD25, Daclizumab, Zenapax, therapeutic antibody, immune system, Immune system-Cytokine complex; Immune system/Cytokine
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_guinier46.20
回转半径 Rg (电子) rg_electron45.92
零角强度 I(0) i0221627000.00
分子量 molecular_weight118550.0 kDa
排除体积 excluded_volume146860 ų
包络体积 envelope_volume236170 ų
水化壳体积 shell_volume44494 ų
包络直径 envelope_diameter154.3
壳层 Rg shell_rg47.87
包络 Rg envelope_rg44.80
形状 Rg shape_rg45.89
总 Rg total_rg46.10
总原子数 total_atoms8324
残基数 n_residues1086
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 dmax154.8
Rg (实空间) rg_real46.42
Rg 误差 (实空间) rg_real_error1.78
I(0) (实空间) i0_real2.2160e+08
I(0) 误差 (实空间) i0_real_error4.3650e+06
Rg (倒空间) rg_reciprocal46.21
I(0) (倒空间) i0_reciprocal221600000.0000
解质量估计 total_estimate0.8632
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary36.4
偏度 Skewness skewness0.263
峰度 Kurtosis kurtosis-0.835
角度范围 angular_range— – 0.1700 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha18000000.0000
实空间数据点数 n_real_points35
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.883

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) 22 domains

SCOP 2.08 (10 domains)

结构域编号 domain_idd3nfpa_
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd3nfpb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd3nfpb2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
结构域编号 domain_idd3nfph_
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd3nfpi1
类 Class classg — Small proteins
折叠类型 Fold foldg.18 — Complement control module/SCR domain
超家族 Superfamily superfamilyg.18.1 — Complement control module/SCR domain
家族 Family familyg.18.1.1 — Complement control module/SCR domain
结构域编号 domain_idd3nfpi2
类 Class classg — Small proteins
折叠类型 Fold foldg.18 — Complement control module/SCR domain
超家族 Superfamily superfamilyg.18.1 — Complement control module/SCR domain
家族 Family familyg.18.1.1 — Complement control module/SCR domain
结构域编号 domain_idd3nfpk1
类 Class classg — Small proteins
折叠类型 Fold foldg.18 — Complement control module/SCR domain
超家族 Superfamily superfamilyg.18.1 — Complement control module/SCR domain
家族 Family familyg.18.1.1 — Complement control module/SCR domain
结构域编号 domain_idd3nfpk2
类 Class classg — Small proteins
折叠类型 Fold foldg.18 — Complement control module/SCR domain
超家族 Superfamily superfamilyg.18.1 — Complement control module/SCR domain
家族 Family familyg.18.1.1 — Complement control module/SCR domain
结构域编号 domain_idd3nfpl1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd3nfpl2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (12 domains)

结构域编号 domain_id3nfpA01
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_id3nfpA02
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_id3nfpB01
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_id3nfpB02
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_id3nfpH01
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_id3nfpH02
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_id3nfpI01
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_id3nfpI02
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_id3nfpK01
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_id3nfpK02
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_id3nfpL01
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_id3nfpL02
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)