1h7x
Dihydropyrimidine dehydrogenase (DPD) from pig, ternary complex of a mutant enzyme (C671A), NADPH and 5-fluorouracil
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 | 1h7x |
| 沉积日期 deposition_date | 2001-01-19 |
| 结构标题 title | Dihydropyrimidine dehydrogenase (DPD) from pig, ternary complex of a mutant enzyme (C671A), NADPH and 5-fluorouracil |
| 关键词 keywords | ELECTRON TRANSFER, FLAVIN, IRON-SULFUR CLUSTERS, PYRIMIDINE CATABOLISM, 5-FLUOROURACIL DEGRADATION, OXIDOREDUCTASE; ELECTRON TRANSFER |
| 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 | 56.02 Å |
| 回转半径 Rg (电子) rg_electron | 56.44 Å |
| 零角强度 I(0) i0 | 3064960000.00 |
| 分子量 molecular_weight | 456950.0 kDa |
| 排除体积 excluded_volume | 567970 ų |
| 包络体积 envelope_volume | 742410 ų |
| 水化壳体积 shell_volume | 108620 ų |
| 包络直径 envelope_diameter | 198.1 Å |
| 壳层 Rg shell_rg | 58.58 Å |
| 包络 Rg envelope_rg | 56.30 Å |
| 形状 Rg shape_rg | 56.54 Å |
| 总 Rg total_rg | 56.14 Å |
| 总原子数 total_atoms | 31748 |
| 残基数 n_residues | 4073 |
| 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 | 196.9 Å |
| Rg (实空间) rg_real | 56.26 Å |
| Rg 误差 (实空间) rg_real_error | 2.22 Å |
| I(0) (实空间) i0_real | 3.0650e+09 |
| I(0) 误差 (实空间) i0_real_error | 6.5520e+07 |
| Rg (倒空间) rg_reciprocal | 55.80 Å |
| I(0) (倒空间) i0_reciprocal | 3063000000.0000 |
| 解质量估计 total_estimate | 0.6214 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 56.3 Å |
| 偏度 Skewness skewness | 0.461 |
| 峰度 Kurtosis kurtosis | -0.393 |
| 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 | 376000000.0000 |
| 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: 0.758; Stabil: 1.000; Sysdev: 0.041; Positv: 1.000; Valcen: 0.965; Smooth: 0.713 |
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) 40 domains
SCOP 2.08 (20 domains)
| 结构域编号 domain_id | d1h7xa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.1 — Globin-like |
| 超家族 Superfamily superfamily | a.1.2 — alpha-helical ferredoxin |
| 家族 Family family | a.1.2.2 — Dihydropyrimidine dehydrogenase, N-terminal domain |
| 结构域编号 domain_id | d1h7xa2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.4 — FMN-linked oxidoreductases |
| 家族 Family family | c.1.4.1 — FMN-linked oxidoreductases |
| 结构域编号 domain_id | d1h7xa3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.1 — C-terminal domain of adrenodoxin reductase-like |
| 结构域编号 domain_id | d1h7xa4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.4 — Nucleotide-binding domain |
| 超家族 Superfamily superfamily | c.4.1 — Nucleotide-binding domain |
| 家族 Family family | c.4.1.1 — N-terminal domain of adrenodoxin reductase-like |
| 结构域编号 domain_id | d1h7xa5 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.1 — 4Fe-4S ferredoxins |
| 家族 Family family | d.58.1.5 — Ferredoxin domains from multidomain proteins |
| 结构域编号 domain_id | d1h7xb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.1 — Globin-like |
| 超家族 Superfamily superfamily | a.1.2 — alpha-helical ferredoxin |
| 家族 Family family | a.1.2.2 — Dihydropyrimidine dehydrogenase, N-terminal domain |
| 结构域编号 domain_id | d1h7xb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.4 — FMN-linked oxidoreductases |
| 家族 Family family | c.1.4.1 — FMN-linked oxidoreductases |
| 结构域编号 domain_id | d1h7xb3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.1 — C-terminal domain of adrenodoxin reductase-like |
| 结构域编号 domain_id | d1h7xb4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.4 — Nucleotide-binding domain |
| 超家族 Superfamily superfamily | c.4.1 — Nucleotide-binding domain |
| 家族 Family family | c.4.1.1 — N-terminal domain of adrenodoxin reductase-like |
| 结构域编号 domain_id | d1h7xb5 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.1 — 4Fe-4S ferredoxins |
| 家族 Family family | d.58.1.5 — Ferredoxin domains from multidomain proteins |
| 结构域编号 domain_id | d1h7xc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.1 — Globin-like |
| 超家族 Superfamily superfamily | a.1.2 — alpha-helical ferredoxin |
| 家族 Family family | a.1.2.2 — Dihydropyrimidine dehydrogenase, N-terminal domain |
| 结构域编号 domain_id | d1h7xc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.4 — FMN-linked oxidoreductases |
| 家族 Family family | c.1.4.1 — FMN-linked oxidoreductases |
| 结构域编号 domain_id | d1h7xc3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.1 — C-terminal domain of adrenodoxin reductase-like |
| 结构域编号 domain_id | d1h7xc4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.4 — Nucleotide-binding domain |
| 超家族 Superfamily superfamily | c.4.1 — Nucleotide-binding domain |
| 家族 Family family | c.4.1.1 — N-terminal domain of adrenodoxin reductase-like |
| 结构域编号 domain_id | d1h7xc5 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.1 — 4Fe-4S ferredoxins |
| 家族 Family family | d.58.1.5 — Ferredoxin domains from multidomain proteins |
| 结构域编号 domain_id | d1h7xd1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.1 — Globin-like |
| 超家族 Superfamily superfamily | a.1.2 — alpha-helical ferredoxin |
| 家族 Family family | a.1.2.2 — Dihydropyrimidine dehydrogenase, N-terminal domain |
| 结构域编号 domain_id | d1h7xd2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.4 — FMN-linked oxidoreductases |
| 家族 Family family | c.1.4.1 — FMN-linked oxidoreductases |
| 结构域编号 domain_id | d1h7xd3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.1 — C-terminal domain of adrenodoxin reductase-like |
| 结构域编号 domain_id | d1h7xd4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.4 — Nucleotide-binding domain |
| 超家族 Superfamily superfamily | c.4.1 — Nucleotide-binding domain |
| 家族 Family family | c.4.1.1 — N-terminal domain of adrenodoxin reductase-like |
| 结构域编号 domain_id | d1h7xd5 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.1 — 4Fe-4S ferredoxins |
| 家族 Family family | d.58.1.5 — Ferredoxin domains from multidomain proteins |
CATH v4.4 (20 domains)
| 结构域编号 domain_id | 1h7xA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1h7xA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1060 — Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Alpha-helical ferredoxin |
| 结构域编号 domain_id | 1h7xA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1h7xA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1h7xA05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 70 — Aldolase class I |
| 结构域编号 domain_id | 1h7xB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1h7xB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1060 — Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Alpha-helical ferredoxin |
| 结构域编号 domain_id | 1h7xB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1h7xB04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1h7xB05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 70 — Aldolase class I |
| 结构域编号 domain_id | 1h7xC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1h7xC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1060 — Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Alpha-helical ferredoxin |
| 结构域编号 domain_id | 1h7xC03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1h7xC04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1h7xC05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 70 — Aldolase class I |
| 结构域编号 domain_id | 1h7xD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1h7xD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1060 — Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Alpha-helical ferredoxin |
| 结构域编号 domain_id | 1h7xD03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1h7xD04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1h7xD05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 70 — Aldolase class I |