1y2k
;Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 3,5-dimethyl-1-(3-nitro-phenyl)-1H-pyrazole-4-carboxylic acid ethyl ester ;
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 | 1y2k |
| 沉积日期 deposition_date | 2004-11-22 |
| 结构标题 title | ;Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 3,5-dimethyl-1-(3-nitro-phenyl)-1H-pyrazole-4-carboxylic acid ethyl ester ; |
| 关键词 keywords | Phosphodiesterase, PDE, PDE4D, Pyrazole, Hydrolase; HYDROLASE |
| 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 | 28.96 Å |
| 回转半径 Rg (电子) rg_electron | 28.10 Å |
| 零角强度 I(0) i0 | 97604900.00 |
| 分子量 molecular_weight | 77465.0 kDa |
| 排除体积 excluded_volume | 96811 ų |
| 包络体积 envelope_volume | 117550 ų |
| 水化壳体积 shell_volume | 34232 ų |
| 包络直径 envelope_diameter | 98.6 Å |
| 壳层 Rg shell_rg | 35.87 Å |
| 包络 Rg envelope_rg | 28.20 Å |
| 形状 Rg shape_rg | 28.13 Å |
| 总 Rg total_rg | 28.78 Å |
| 总原子数 total_atoms | 5431 |
| 残基数 n_residues | 648 |
| 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 | 93.3 Å |
| Rg (实空间) rg_real | 28.93 Å |
| Rg 误差 (实空间) rg_real_error | 0.64 Å |
| I(0) (实空间) i0_real | 9.7600e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.3500e+06 |
| Rg (倒空间) rg_reciprocal | 28.94 Å |
| I(0) (倒空间) i0_reciprocal | 97610000.0000 |
| 解质量估计 total_estimate | 0.8985 |
| 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 | 32.2 Å |
| 偏度 Skewness skewness | 0.300 |
| 峰度 Kurtosis kurtosis | -0.481 |
| 角度范围 angular_range | — – 0.2750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 24280000.0000 |
| 实空间数据点数 n_real_points | 56 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.956 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1y2ka_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.211 — HD-domain/PDEase-like |
| 超家族 Superfamily superfamily | a.211.1 — HD-domain/PDEase-like |
| 家族 Family family | a.211.1.2 — PDEase |
| 结构域编号 domain_id | d1y2kb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.211 — HD-domain/PDEase-like |
| 超家族 Superfamily superfamily | a.211.1 — HD-domain/PDEase-like |
| 家族 Family family | a.211.1.2 — PDEase |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1y2kA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b |
| 同源超家族 H-superfamily homologous superfamily | 10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain |
| 结构域编号 domain_id | 1y2kB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b |
| 同源超家族 H-superfamily homologous superfamily | 10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain |