2e0a
Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with AMPPNP
SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
1. 结构基本信息 1. Structure Basics
| 条目编号 entry_id | 2e0a |
| 沉积日期 deposition_date | 2006-10-03 |
| 结构标题 title | Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with AMPPNP |
| 关键词 keywords | ;PDK4, kinase, ATP-binding, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSFERASE ;; TRANSFERASE |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 30.16 Å |
| 回转半径 Rg (电子) rg_electron | 29.20 Å |
| 零角强度 I(0) i0 | 105465000.00 |
| 分子量 molecular_weight | 82002.0 kDa |
| 排除体积 excluded_volume | 102910 ų |
| 包络体积 envelope_volume | 126440 ų |
| 水化壳体积 shell_volume | 36051 ų |
| 包络直径 envelope_diameter | 105.5 Å |
| 壳层 Rg shell_rg | 36.50 Å |
| 包络 Rg envelope_rg | 28.99 Å |
| 形状 Rg shape_rg | 29.21 Å |
| 总 Rg total_rg | 29.86 Å |
| 总原子数 total_atoms | 5768 |
| 残基数 n_residues | 711 |
| 球谐函数阶数 n_harmonics | 20 |
| q 范围 q_range | — – 0.5000 Å−1 |
| 数据点数 n_points | 101 |
| 壳层类型 shell_type | directional |
| 溶剂电子密度 solvent_density | 0.3340 e/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 99.6 Å |
| Rg (实空间) rg_real | 30.14 Å |
| Rg 误差 (实空间) rg_real_error | 0.61 Å |
| I(0) (实空间) i0_real | 1.0550e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.3960e+06 |
| Rg (倒空间) rg_reciprocal | 30.15 Å |
| I(0) (倒空间) i0_reciprocal | 105500000.0000 |
| 解质量估计 total_estimate | 0.8945 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 35.7 Å |
| 偏度 Skewness skewness | 0.315 |
| 峰度 Kurtosis kurtosis | -0.341 |
| 角度范围 angular_range | — – 0.2650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 20320000.0000 |
| 实空间数据点数 n_real_points | 54 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.960 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2e0aa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain |
| 家族 Family family | a.29.5.0 — automated matches |
| 结构域编号 domain_id | d2e0aa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase |
| 超家族 Superfamily superfamily | d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase |
| 家族 Family family | d.122.1.0 — automated matches |
| 结构域编号 domain_id | d2e0ab1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain |
| 家族 Family family | a.29.5.0 — automated matches |
| 结构域编号 domain_id | d2e0ab2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase |
| 超家族 Superfamily superfamily | d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase |
| 家族 Family family | d.122.1.0 — automated matches |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2e0aA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain |
| 结构域编号 domain_id | 2e0aA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 565 — Heat Shock Protein 90 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Histidine kinase-like ATPase, C-terminal domain |
| 结构域编号 domain_id | 2e0aB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain |
| 结构域编号 domain_id | 2e0aB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 565 — Heat Shock Protein 90 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Histidine kinase-like ATPase, C-terminal domain |