6xm2

The structure of the 4A11.v7 antibody in complex with human TGFb2

Method: X-RAY DIFFRACTION Dmax: 156.3 Å Quality: GOOD

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

Transforming growth factor beta-2

Homo sapiens

UniProt P61812

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 × 6 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 K; UniProt 303–414 链 L; UniProt 303–414 片段:mature domain 4A11.v7 kappa light chain Fab (VL-CL) humanized × 2 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;292 K;20% PEG 1000, 0.1 M Tris pH8.5 分辨率 1.91 Å R-free 0.244
2 蛋白异源复合物 异源复合物 蛋白 × 6 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 I; UniProt 303–414 链 J; UniProt 303–414 片段:mature domain 4A11.v7 kappa light chain Fab (VL-CL) humanized × 2 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;292 K;20% PEG 1000, 0.1 M Tris pH8.5 分辨率 1.91 Å R-free 0.244

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、10 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 TGFB2_HUMAN
Isoform
PDB实体 3
链与序列区间 作者链 I; PDB构建体 1–112; UniProt 303–414 作者链 J; PDB构建体 1–112; UniProt 303–414 作者链 K; PDB构建体 1–112; UniProt 303–414 作者链 L; PDB构建体 1–112; UniProt 303–414

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 6xm2

P(r) 距离分布 P(r) Distribution

P(r) distribution for 6xm2
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id6xm2
沉积日期 deposition_date2020-06-29
结构标题 titleThe structure of the 4A11.v7 antibody in complex with human TGFb2
关键词 keywordsTGFb antibody, CYTOKINE, CYTOKINE-IMMUNE SYSTEM complex; CYTOKINE/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_guinier45.36
回转半径 Rg (电子) rg_electron45.18
零角强度 I(0) i0813446000.00
分子量 molecular_weight233190.0 kDa
排除体积 excluded_volume290720 ų
包络体积 envelope_volume410510 ų
水化壳体积 shell_volume76218 ų
包络直径 envelope_diameter168.1
壳层 Rg shell_rg49.67
包络 Rg envelope_rg44.00
形状 Rg shape_rg45.17
总 Rg total_rg45.43
总原子数 total_atoms16409
残基数 n_residues2179
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 dmax156.3
Rg (实空间) rg_real45.25
Rg 误差 (实空间) rg_real_error2.11
I(0) (实空间) i0_real8.1340e+08
I(0) 误差 (实空间) i0_real_error1.7660e+07
Rg (倒空间) rg_reciprocal45.36
I(0) (倒空间) i0_reciprocal813500000.0000
解质量估计 total_estimate0.8718
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary58.1
偏度 Skewness skewness0.275
峰度 Kurtosis kurtosis-0.280
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_alpha52860000.0000
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: 0.789; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.962

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) 28 domains

SCOP 2.08 (12 domains)

结构域编号 domain_idd6xm2a_
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_idd6xm2b_
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_idd6xm2c_
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_idd6xm2d_
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_idd6xm2e_
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_idd6xm2f_
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_idd6xm2g_
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_idd6xm2h_
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_idd6xm2i_
类 Class classg — Small proteins
折叠类型 Fold foldg.17 — Cystine-knot cytokines
超家族 Superfamily superfamilyg.17.1 — Cystine-knot cytokines
家族 Family familyg.17.1.2 — Transforming growth factor (TGF)-beta
结构域编号 domain_idd6xm2j_
类 Class classg — Small proteins
折叠类型 Fold foldg.17 — Cystine-knot cytokines
超家族 Superfamily superfamilyg.17.1 — Cystine-knot cytokines
家族 Family familyg.17.1.2 — Transforming growth factor (TGF)-beta
结构域编号 domain_idd6xm2k_
类 Class classg — Small proteins
折叠类型 Fold foldg.17 — Cystine-knot cytokines
超家族 Superfamily superfamilyg.17.1 — Cystine-knot cytokines
家族 Family familyg.17.1.2 — Transforming growth factor (TGF)-beta
结构域编号 domain_idd6xm2l_
类 Class classg — Small proteins
折叠类型 Fold foldg.17 — Cystine-knot cytokines
超家族 Superfamily superfamilyg.17.1 — Cystine-knot cytokines
家族 Family familyg.17.1.2 — Transforming growth factor (TGF)-beta

CATH v4.4 (16 domains)

结构域编号 domain_id6xm2A01
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_id6xm2A02
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_id6xm2B01
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_id6xm2B02
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_id6xm2C01
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_id6xm2C02
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_id6xm2D01
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_id6xm2D02
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_id6xm2E01
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_id6xm2E02
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_id6xm2F01
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_id6xm2F02
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_id6xm2G01
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_id6xm2G02
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_id6xm2H01
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_id6xm2H02
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

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