4md9

Crystal Structure of symmetric CK2 holoenzyme with mutated alpha subunit (F121E truncated at aa 336)

Method: X-RAY DIFFRACTION Dmax: 214.0 Å Quality: GOOD

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

Casein kinase II subunit beta

Homo sapiens

UniProt P67870

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 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 A; UniProt 1–215 链 B; UniProt 1–215 未记录 Casein kinase II subunit alpha × 2 (P68400) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K 分辨率 3.50 Å R-free 0.259
2 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 C; UniProt 1–215 链 D; UniProt 1–215 未记录 Casein kinase II subunit alpha × 2 (P68400) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K 分辨率 3.50 Å R-free 0.259
3 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 N; UniProt 1–215 链 O; UniProt 1–215 未记录 Casein kinase II subunit alpha × 2 (P68400) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K 分辨率 3.50 Å R-free 0.259
4 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 I; UniProt 1–215 链 J; UniProt 1–215 未记录 Casein kinase II subunit alpha × 2 (P68400) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K 分辨率 3.50 Å R-free 0.259

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 8 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 CSK2B_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–215; UniProt 1–215 作者链 B; PDB构建体 1–215; UniProt 1–215 作者链 C; PDB构建体 1–215; UniProt 1–215 作者链 D; PDB构建体 1–215; UniProt 1–215 作者链 I; PDB构建体 1–215; UniProt 1–215 作者链 J; PDB构建体 1–215; UniProt 1–215 作者链 N; PDB构建体 1–215; UniProt 1–215 作者链 O; PDB构建体 1–215; UniProt 1–215

Casein kinase II subunit alpha

Homo sapiens

UniProt P68400

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 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 E; UniProt 1–336 链 F; UniProt 1–336 片段:kinase domain (UNP residues 1-336) 突变:F121E Casein kinase II subunit beta × 2 (P67870) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K 分辨率 3.50 Å R-free 0.259
2 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 H; UniProt 1–336 链 K; UniProt 1–336 片段:kinase domain (UNP residues 1-336) 突变:F121E Casein kinase II subunit beta × 2 (P67870) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K 分辨率 3.50 Å R-free 0.259
3 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 G; UniProt 1–336 链 P; UniProt 1–336 片段:kinase domain (UNP residues 1-336) 突变:F121E Casein kinase II subunit beta × 2 (P67870) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K 分辨率 3.50 Å R-free 0.259
4 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 L; UniProt 1–336 链 M; UniProt 1–336 片段:kinase domain (UNP residues 1-336) 突变:F121E Casein kinase II subunit beta × 2 (P67870) ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.5;277 K;20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K 分辨率 3.50 Å R-free 0.259

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 313 个其他 PDB 条目、445 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 CSK21_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 E; PDB构建体 1–336; UniProt 1–336 作者链 F; PDB构建体 1–336; UniProt 1–336 作者链 G; PDB构建体 1–336; UniProt 1–336 作者链 H; PDB构建体 1–336; UniProt 1–336 作者链 K; PDB构建体 1–336; UniProt 1–336 作者链 L; PDB构建体 1–336; UniProt 1–336 作者链 M; PDB构建体 1–336; UniProt 1–336 作者链 P; PDB构建体 1–336; UniProt 1–336

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 4md9

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4md9
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id4md9
沉积日期 deposition_date2013-08-22
结构标题 titleCrystal Structure of symmetric CK2 holoenzyme with mutated alpha subunit (F121E truncated at aa 336)
关键词 keywordsprotein serine/threonine kinase, TRANSFERASE; TRANSFERASE
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_guinier70.10
回转半径 Rg (电子) rg_electron70.43
零角强度 I(0) i03459110000.00
分子量 molecular_weight497470.0 kDa
排除体积 excluded_volume622380 ų
包络体积 envelope_volume1039100 ų
水化壳体积 shell_volume131710 ų
包络直径 envelope_diameter249.7
壳层 Rg shell_rg63.72
包络 Rg envelope_rg67.78
形状 Rg shape_rg70.48
总 Rg total_rg70.14
总原子数 total_atoms35073
残基数 n_residues4203
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 dmax214.0
Rg (实空间) rg_real69.81
Rg 误差 (实空间) rg_real_error1.29
I(0) (实空间) i0_real3.4480e+09
I(0) 误差 (实空间) i0_real_error6.6760e+07
Rg (倒空间) rg_reciprocal69.28
I(0) (倒空间) i0_reciprocal3452000000.0000
解质量估计 total_estimate0.8606
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary77.8
偏度 Skewness skewness0.497
峰度 Kurtosis kurtosis-0.052
角度范围 angular_range— – 0.1100 −1
当前正则化参数 α current_alpha0.0153
最高正则化参数 α highest_alpha130900000.0000
实空间数据点数 n_real_points23
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.472

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

6. 实体与聚合物信息 Entities & Polymers (3)

7. 折叠分类 (SCOP + CATH) 32 domains

CATH v4.4 (32 domains)

结构域编号 domain_id4md9A01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
同源超家族 H-superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
结构域编号 domain_id4md9A02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id4md9B01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
同源超家族 H-superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
结构域编号 domain_id4md9B02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id4md9C01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
同源超家族 H-superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
结构域编号 domain_id4md9C02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id4md9D01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
同源超家族 H-superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
结构域编号 domain_id4md9D02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id4md9E01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id4md9E02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id4md9F01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id4md9F02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id4md9G01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id4md9G02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id4md9H01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id4md9H02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id4md9I01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
同源超家族 H-superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
结构域编号 domain_id4md9I02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id4md9J01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
同源超家族 H-superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
结构域编号 domain_id4md9J02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id4md9K01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id4md9K02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id4md9L01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id4md9L02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id4md9M01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id4md9M02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id4md9N01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
同源超家族 H-superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
结构域编号 domain_id4md9N02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id4md9O01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology1820 — protein kinase ck2 holoenzyme, chain C, domain 1
同源超家族 H-superfamily homologous superfamily10 — protein kinase ck2 holoenzyme, chain C, domain 1
结构域编号 domain_id4md9O02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id4md9P01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id4md9P02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1

8. 引用文献 (1)

9. 文件与曲线 (10)