1mkd
crystal structure of PDE4D catalytic domain and zardaverine complex
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 | 1mkd |
| 沉积日期 deposition_date | 2002-08-29 |
| 结构标题 title | crystal structure of PDE4D catalytic domain and zardaverine complex |
| 关键词 keywords | PDE, Zardaverine, 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 | 56.74 Å |
| 回转半径 Rg (电子) rg_electron | 56.54 Å |
| 零角强度 I(0) i0 | 2998260000.00 |
| 分子量 molecular_weight | 456310.0 kDa |
| 排除体积 excluded_volume | 568910 ų |
| 包络体积 envelope_volume | 805510 ų |
| 水化壳体积 shell_volume | 117650 ų |
| 包络直径 envelope_diameter | 195.5 Å |
| 壳层 Rg shell_rg | 60.01 Å |
| 包络 Rg envelope_rg | 55.03 Å |
| 形状 Rg shape_rg | 56.55 Å |
| 总 Rg total_rg | 56.58 Å |
| 总原子数 total_atoms | 32052 |
| 残基数 n_residues | 3936 |
| 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 | 185.0 Å |
| Rg (实空间) rg_real | 56.78 Å |
| Rg 误差 (实空间) rg_real_error | 1.58 Å |
| I(0) (实空间) i0_real | 2.9980e+09 |
| I(0) 误差 (实空间) i0_real_error | 5.7330e+07 |
| Rg (倒空间) rg_reciprocal | 56.68 Å |
| I(0) (倒空间) i0_reciprocal | 2998000000.0000 |
| 解质量估计 total_estimate | 0.8376 |
| 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 | 59.5 Å |
| 偏度 Skewness skewness | 0.385 |
| 峰度 Kurtosis kurtosis | -0.416 |
| 角度范围 angular_range | — – 0.1400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 325700000.0000 |
| 实空间数据点数 n_real_points | 29 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.424 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 24 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1mkda_ |
| 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 | d1mkdb_ |
| 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 | d1mkdc_ |
| 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 | d1mkdd_ |
| 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 | d1mkde_ |
| 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 | d1mkdf_ |
| 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 | d1mkdg_ |
| 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 | d1mkdh_ |
| 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 | d1mkdi_ |
| 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 | d1mkdj_ |
| 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 | d1mkdk_ |
| 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 | d1mkdl_ |
| 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 (12 domains)
| 结构域编号 domain_id | 1mkdA00 |
| 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 | 1mkdB00 |
| 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 | 1mkdC00 |
| 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 | 1mkdD00 |
| 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 | 1mkdE00 |
| 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 | 1mkdF00 |
| 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 | 1mkdG00 |
| 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 | 1mkdH00 |
| 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 | 1mkdI00 |
| 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 | 1mkdJ00 |
| 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 | 1mkdK00 |
| 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 | 1mkdL00 |
| 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 |