1yvh
Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide
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 | 1yvh |
| 沉积日期 deposition_date | 2005-02-15 |
| 结构标题 title | Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide |
| 关键词 keywords | X-RAY CRYSTALLOGRAPHY; PHOSPHOTYROSINE; ADAPTER PROTEIN, LIGASE, SIGNALING PROTEIN, IMMUNE SYSTEM; LIGASE,SIGNALING PROTEIN,IMMUNE SYSTEM |
| 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 | 21.33 Å |
| 回转半径 Rg (电子) rg_electron | 20.25 Å |
| 零角强度 I(0) i0 | 21378900.00 |
| 分子量 molecular_weight | 36391.0 kDa |
| 排除体积 excluded_volume | 46040 ų |
| 包络体积 envelope_volume | 52832 ų |
| 水化壳体积 shell_volume | 21641 ų |
| 包络直径 envelope_diameter | 68.4 Å |
| 壳层 Rg shell_rg | 26.77 Å |
| 包络 Rg envelope_rg | 20.41 Å |
| 形状 Rg shape_rg | 20.24 Å |
| 总 Rg total_rg | 21.14 Å |
| 总原子数 total_atoms | 2566 |
| 残基数 n_residues | 312 |
| 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 | 68.8 Å |
| Rg (实空间) rg_real | 21.22 Å |
| Rg 误差 (实空间) rg_real_error | 0.43 Å |
| I(0) (实空间) i0_real | 2.1380e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.7800e+05 |
| Rg (倒空间) rg_reciprocal | 21.24 Å |
| I(0) (倒空间) i0_reciprocal | 21380000.0000 |
| 解质量估计 total_estimate | 0.8958 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 25.3 Å |
| 偏度 Skewness skewness | 0.179 |
| 峰度 Kurtosis kurtosis | -0.459 |
| 角度范围 angular_range | — – 0.3750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 6587000.0000 |
| 实空间数据点数 n_real_points | 69 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996 |
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) 6 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1yvha1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.39 — EF Hand-like |
| 超家族 Superfamily superfamily | a.39.1 — EF-hand |
| 家族 Family family | a.39.1.7 — EF-hand modules in multidomain proteins |
| 结构域编号 domain_id | d1yvha2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.48 — N-cbl like |
| 超家族 Superfamily superfamily | a.48.1 — N-terminal domain of cbl (N-cbl) |
| 家族 Family family | a.48.1.1 — N-terminal domain of cbl (N-cbl) |
| 结构域编号 domain_id | d1yvha3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.93 — SH2-like |
| 超家族 Superfamily superfamily | d.93.1 — SH2 domain |
| 家族 Family family | d.93.1.1 — SH2 domain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1yvhA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 930 — Transcription Elongation Factor S-II; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Adaptor protein Cbl, N-terminal domain |
| 结构域编号 domain_id | 1yvhA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 238 — Recoverin; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — EF-hand |
| 结构域编号 domain_id | 1yvhA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 505 — SHC Adaptor Protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — SH2 domain |