1r4n
APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP
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 | 1r4n |
| 沉积日期 deposition_date | 2003-10-07 |
| 结构标题 title | APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP |
| 关键词 keywords | CELL CYCLE; CELL CYCLE |
| 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 | 55.53 Å |
| 回转半径 Rg (电子) rg_electron | 55.16 Å |
| 零角强度 I(0) i0 | 2868490000.00 |
| 分子量 molecular_weight | 451050.0 kDa |
| 排除体积 excluded_volume | 564390 ų |
| 包络体积 envelope_volume | 806550 ų |
| 水化壳体积 shell_volume | 116060 ų |
| 包络直径 envelope_diameter | 196.7 Å |
| 壳层 Rg shell_rg | 63.18 Å |
| 包络 Rg envelope_rg | 54.29 Å |
| 形状 Rg shape_rg | 55.16 Å |
| 总 Rg total_rg | 55.35 Å |
| 总原子数 total_atoms | 31744 |
| 残基数 n_residues | 4040 |
| 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 | 180.6 Å |
| Rg (实空间) rg_real | 55.35 Å |
| Rg 误差 (实空间) rg_real_error | 1.45 Å |
| I(0) (实空间) i0_real | 2.8680e+09 |
| I(0) 误差 (实空间) i0_real_error | 5.6900e+07 |
| Rg (倒空间) rg_reciprocal | 55.66 Å |
| I(0) (倒空间) i0_reciprocal | 2870000000.0000 |
| 解质量估计 total_estimate | 0.8829 |
| 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 | 77.4 Å |
| 偏度 Skewness skewness | 0.185 |
| 峰度 Kurtosis kurtosis | -0.405 |
| 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 | 517400000.0000 |
| 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: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.810 |
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) 32 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1r4na_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.111 — Activating enzymes of the ubiquitin-like proteins |
| 超家族 Superfamily superfamily | c.111.1 — Activating enzymes of the ubiquitin-like proteins |
| 家族 Family family | c.111.1.2 — Ubiquitin activating enzymes (UBA) |
| 结构域编号 domain_id | d1r4nb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.111 — Activating enzymes of the ubiquitin-like proteins |
| 超家族 Superfamily superfamily | c.111.1 — Activating enzymes of the ubiquitin-like proteins |
| 家族 Family family | c.111.1.2 — Ubiquitin activating enzymes (UBA) |
| 结构域编号 domain_id | d1r4nc_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.111 — Activating enzymes of the ubiquitin-like proteins |
| 超家族 Superfamily superfamily | c.111.1 — Activating enzymes of the ubiquitin-like proteins |
| 家族 Family family | c.111.1.2 — Ubiquitin activating enzymes (UBA) |
| 结构域编号 domain_id | d1r4nd_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.111 — Activating enzymes of the ubiquitin-like proteins |
| 超家族 Superfamily superfamily | c.111.1 — Activating enzymes of the ubiquitin-like proteins |
| 家族 Family family | c.111.1.2 — Ubiquitin activating enzymes (UBA) |
| 结构域编号 domain_id | d1r4ne_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.111 — Activating enzymes of the ubiquitin-like proteins |
| 超家族 Superfamily superfamily | c.111.1 — Activating enzymes of the ubiquitin-like proteins |
| 家族 Family family | c.111.1.2 — Ubiquitin activating enzymes (UBA) |
| 结构域编号 domain_id | d1r4nf_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.111 — Activating enzymes of the ubiquitin-like proteins |
| 超家族 Superfamily superfamily | c.111.1 — Activating enzymes of the ubiquitin-like proteins |
| 家族 Family family | c.111.1.2 — Ubiquitin activating enzymes (UBA) |
| 结构域编号 domain_id | d1r4ng_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.111 — Activating enzymes of the ubiquitin-like proteins |
| 超家族 Superfamily superfamily | c.111.1 — Activating enzymes of the ubiquitin-like proteins |
| 家族 Family family | c.111.1.2 — Ubiquitin activating enzymes (UBA) |
| 结构域编号 domain_id | d1r4nh_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.111 — Activating enzymes of the ubiquitin-like proteins |
| 超家族 Superfamily superfamily | c.111.1 — Activating enzymes of the ubiquitin-like proteins |
| 家族 Family family | c.111.1.2 — Ubiquitin activating enzymes (UBA) |
| 结构域编号 domain_id | d1r4ni_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.1 — Ubiquitin-related |
| 结构域编号 domain_id | d1r4nj_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.1 — Ubiquitin-related |
| 结构域编号 domain_id | d1r4nk_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.1 — Ubiquitin-related |
| 结构域编号 domain_id | d1r4nl_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.1 — Ubiquitin-like |
| 家族 Family family | d.15.1.1 — Ubiquitin-related |
CATH v4.4 (20 domains)
| 结构域编号 domain_id | 1r4nA01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r4nB01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r4nB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 |
| 结构域编号 domain_id | 1r4nB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 260 — NEDD8-activating enzyme E1, catalytic subunit |
| 结构域编号 domain_id | 1r4nC01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r4nD01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r4nD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 |
| 结构域编号 domain_id | 1r4nD03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 260 — NEDD8-activating enzyme E1, catalytic subunit |
| 结构域编号 domain_id | 1r4nE01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r4nF01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r4nF02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 |
| 结构域编号 domain_id | 1r4nF03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 260 — NEDD8-activating enzyme E1, catalytic subunit |
| 结构域编号 domain_id | 1r4nG01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r4nH01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r4nH02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 |
| 结构域编号 domain_id | 1r4nH03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 260 — NEDD8-activating enzyme E1, catalytic subunit |
| 结构域编号 domain_id | 1r4nI00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |
| 结构域编号 domain_id | 1r4nJ00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |
| 结构域编号 domain_id | 1r4nK00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |
| 结构域编号 domain_id | 1r4nL00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 |