2ajb
Porcine dipeptidyl peptidase IV (CD26) in complex with the tripeptide tert-butyl-Gly-L-Pro-L-Ile (tBu-GPI)
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 | 2ajb |
| 沉积日期 deposition_date | 2005-08-01 |
| 结构标题 title | Porcine dipeptidyl peptidase IV (CD26) in complex with the tripeptide tert-butyl-Gly-L-Pro-L-Ile (tBu-GPI) |
| 关键词 keywords | ;Serine protease, dipeptidyl peptidase, alpha/beta-hydrolase, beta-propeller, oxyanion hole, substrate channeling, drug design, diabetes mellitus, flexibility, hydrolase-hydrolase inhibitor complex ;; HYDROLASE/HYDROLASE INHIBITOR |
| 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 | 53.71 Å |
| 回转半径 Rg (电子) rg_electron | 53.26 Å |
| 零角强度 I(0) i0 | 3281520000.00 |
| 分子量 molecular_weight | 322610.0 kDa |
| 排除体积 excluded_volume | 313850 ų |
| 包络体积 envelope_volume | 601230 ų |
| 水化壳体积 shell_volume | 89793 ų |
| 包络直径 envelope_diameter | 166.3 Å |
| 壳层 Rg shell_rg | 61.93 Å |
| 包络 Rg envelope_rg | 51.34 Å |
| 形状 Rg shape_rg | 53.22 Å |
| 总 Rg total_rg | 53.50 Å |
| 总原子数 total_atoms | 24464 |
| 残基数 n_residues | 2912 |
| 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 | 170.7 Å |
| Rg (实空间) rg_real | 53.56 Å |
| Rg 误差 (实空间) rg_real_error | 1.43 Å |
| I(0) (实空间) i0_real | 3.2820e+09 |
| I(0) 误差 (实空间) i0_real_error | 5.9560e+07 |
| Rg (倒空间) rg_reciprocal | 53.81 Å |
| I(0) (倒空间) i0_reciprocal | 3283000000.0000 |
| 解质量估计 total_estimate | 0.8270 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 82.4 Å |
| 偏度 Skewness skewness | 0.084 |
| 峰度 Kurtosis kurtosis | -0.763 |
| 角度范围 angular_range | — – 0.1450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 395000000.0000 |
| 实空间数据点数 n_real_points | 30 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 16 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d2ajba1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.70 — 8-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.70.3 — DPP6 N-terminal domain-like |
| 家族 Family family | b.70.3.1 — DPP6 N-terminal domain-like |
| 结构域编号 domain_id | d2ajba2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.69 — alpha/beta-Hydrolases |
| 超家族 Superfamily superfamily | c.69.1 — alpha/beta-Hydrolases |
| 家族 Family family | c.69.1.24 — DPP6 catalytic domain-like |
| 结构域编号 domain_id | d2ajbb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.70 — 8-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.70.3 — DPP6 N-terminal domain-like |
| 家族 Family family | b.70.3.1 — DPP6 N-terminal domain-like |
| 结构域编号 domain_id | d2ajbb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.69 — alpha/beta-Hydrolases |
| 超家族 Superfamily superfamily | c.69.1 — alpha/beta-Hydrolases |
| 家族 Family family | c.69.1.24 — DPP6 catalytic domain-like |
| 结构域编号 domain_id | d2ajbc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.70 — 8-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.70.3 — DPP6 N-terminal domain-like |
| 家族 Family family | b.70.3.1 — DPP6 N-terminal domain-like |
| 结构域编号 domain_id | d2ajbc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.69 — alpha/beta-Hydrolases |
| 超家族 Superfamily superfamily | c.69.1 — alpha/beta-Hydrolases |
| 家族 Family family | c.69.1.24 — DPP6 catalytic domain-like |
| 结构域编号 domain_id | d2ajbd1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.70 — 8-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.70.3 — DPP6 N-terminal domain-like |
| 家族 Family family | b.70.3.1 — DPP6 N-terminal domain-like |
| 结构域编号 domain_id | d2ajbd2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.69 — alpha/beta-Hydrolases |
| 超家族 Superfamily superfamily | c.69.1 — alpha/beta-Hydrolases |
| 家族 Family family | c.69.1.24 — DPP6 catalytic domain-like |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 2ajbA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 140 — 8 Propeller |
| 拓扑 Topology topology | 10 — Methanol Dehydrogenase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 30 — Dipeptidylpeptidase IV, N-terminal domain |
| 结构域编号 domain_id | 2ajbA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1820 — Alpha/Beta hydrolase fold, catalytic domain |
| 结构域编号 domain_id | 2ajbB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 140 — 8 Propeller |
| 拓扑 Topology topology | 10 — Methanol Dehydrogenase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 30 — Dipeptidylpeptidase IV, N-terminal domain |
| 结构域编号 domain_id | 2ajbB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1820 — Alpha/Beta hydrolase fold, catalytic domain |
| 结构域编号 domain_id | 2ajbC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 140 — 8 Propeller |
| 拓扑 Topology topology | 10 — Methanol Dehydrogenase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 30 — Dipeptidylpeptidase IV, N-terminal domain |
| 结构域编号 domain_id | 2ajbC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1820 — Alpha/Beta hydrolase fold, catalytic domain |
| 结构域编号 domain_id | 2ajbD01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 140 — 8 Propeller |
| 拓扑 Topology topology | 10 — Methanol Dehydrogenase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 30 — Dipeptidylpeptidase IV, N-terminal domain |
| 结构域编号 domain_id | 2ajbD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1820 — Alpha/Beta hydrolase fold, catalytic domain |