1k32
Crystal structure of the tricorn protease
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 | 1k32 |
| 沉积日期 deposition_date | 2001-10-01 |
| 结构标题 title | Crystal structure of the tricorn protease |
| 关键词 keywords | protein degradation, substrate gating, serine protease, beta propeller, proteasome, 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 | 60.15 Å |
| 回转半径 Rg (电子) rg_electron | 59.56 Å |
| 零角强度 I(0) i0 | 6704080000.00 |
| 分子量 molecular_weight | 694970.0 kDa |
| 排除体积 excluded_volume | 869730 ų |
| 包络体积 envelope_volume | 1193100 ų |
| 水化壳体积 shell_volume | 159070 ų |
| 包络直径 envelope_diameter | 188.3 Å |
| 壳层 Rg shell_rg | 69.11 Å |
| 包络 Rg envelope_rg | 57.22 Å |
| 形状 Rg shape_rg | 59.58 Å |
| 总 Rg total_rg | 59.65 Å |
| 总原子数 total_atoms | 49062 |
| 残基数 n_residues | 6138 |
| 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 | 188.0 Å |
| Rg (实空间) rg_real | 59.82 Å |
| Rg 误差 (实空间) rg_real_error | 1.51 Å |
| I(0) (实空间) i0_real | 6.7040e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.4150e+08 |
| Rg (倒空间) rg_reciprocal | 60.41 Å |
| I(0) (倒空间) i0_reciprocal | 6710000000.0000 |
| 解质量估计 total_estimate | 0.6044 |
| 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 | 72.3 Å |
| 偏度 Skewness skewness | 0.107 |
| 峰度 Kurtosis kurtosis | -0.609 |
| 角度范围 angular_range | — – 0.1300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 721600000.0000 |
| 实空间数据点数 n_real_points | 27 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.963; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 54 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1k32a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.3 — Tail specific protease PDZ domain |
| 结构域编号 domain_id | d1k32a2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.7 — Tricorn protease N-terminal domain |
| 家族 Family family | b.68.7.1 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | d1k32a3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.9 — Tricorn protease domain 2 |
| 家族 Family family | b.69.9.1 — Tricorn protease domain 2 |
| 结构域编号 domain_id | d1k32a4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.14 — ClpP/crotonase |
| 超家族 Superfamily superfamily | c.14.1 — ClpP/crotonase |
| 家族 Family family | c.14.1.2 — Tail specific protease, catalytic domain |
| 结构域编号 domain_id | d1k32b1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.3 — Tail specific protease PDZ domain |
| 结构域编号 domain_id | d1k32b2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.7 — Tricorn protease N-terminal domain |
| 家族 Family family | b.68.7.1 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | d1k32b3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.9 — Tricorn protease domain 2 |
| 家族 Family family | b.69.9.1 — Tricorn protease domain 2 |
| 结构域编号 domain_id | d1k32b4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.14 — ClpP/crotonase |
| 超家族 Superfamily superfamily | c.14.1 — ClpP/crotonase |
| 家族 Family family | c.14.1.2 — Tail specific protease, catalytic domain |
| 结构域编号 domain_id | d1k32c1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.3 — Tail specific protease PDZ domain |
| 结构域编号 domain_id | d1k32c2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.7 — Tricorn protease N-terminal domain |
| 家族 Family family | b.68.7.1 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | d1k32c3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.9 — Tricorn protease domain 2 |
| 家族 Family family | b.69.9.1 — Tricorn protease domain 2 |
| 结构域编号 domain_id | d1k32c4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.14 — ClpP/crotonase |
| 超家族 Superfamily superfamily | c.14.1 — ClpP/crotonase |
| 家族 Family family | c.14.1.2 — Tail specific protease, catalytic domain |
| 结构域编号 domain_id | d1k32d1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.3 — Tail specific protease PDZ domain |
| 结构域编号 domain_id | d1k32d2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.7 — Tricorn protease N-terminal domain |
| 家族 Family family | b.68.7.1 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | d1k32d3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.9 — Tricorn protease domain 2 |
| 家族 Family family | b.69.9.1 — Tricorn protease domain 2 |
| 结构域编号 domain_id | d1k32d4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.14 — ClpP/crotonase |
| 超家族 Superfamily superfamily | c.14.1 — ClpP/crotonase |
| 家族 Family family | c.14.1.2 — Tail specific protease, catalytic domain |
| 结构域编号 domain_id | d1k32e1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.3 — Tail specific protease PDZ domain |
| 结构域编号 domain_id | d1k32e2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.7 — Tricorn protease N-terminal domain |
| 家族 Family family | b.68.7.1 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | d1k32e3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.9 — Tricorn protease domain 2 |
| 家族 Family family | b.69.9.1 — Tricorn protease domain 2 |
| 结构域编号 domain_id | d1k32e4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.14 — ClpP/crotonase |
| 超家族 Superfamily superfamily | c.14.1 — ClpP/crotonase |
| 家族 Family family | c.14.1.2 — Tail specific protease, catalytic domain |
| 结构域编号 domain_id | d1k32f1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.36 — PDZ domain-like |
| 超家族 Superfamily superfamily | b.36.1 — PDZ domain-like |
| 家族 Family family | b.36.1.3 — Tail specific protease PDZ domain |
| 结构域编号 domain_id | d1k32f2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.68 — 6-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.68.7 — Tricorn protease N-terminal domain |
| 家族 Family family | b.68.7.1 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | d1k32f3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.9 — Tricorn protease domain 2 |
| 家族 Family family | b.69.9.1 — Tricorn protease domain 2 |
| 结构域编号 domain_id | d1k32f4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.14 — ClpP/crotonase |
| 超家族 Superfamily superfamily | c.14.1 — ClpP/crotonase |
| 家族 Family family | c.14.1.2 — Tail specific protease, catalytic domain |
CATH v4.4 (30 domains)
| 结构域编号 domain_id | 1k32A01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 60 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | 1k32A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 1k32A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 750 — Transcription Regulator spoIIAA |
| 同源超家族 H-superfamily homologous superfamily | 44 — |
| 结构域编号 domain_id | 1k32A04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1k32A05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 226 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 结构域编号 domain_id | 1k32B01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 60 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | 1k32B02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 1k32B03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 750 — Transcription Regulator spoIIAA |
| 同源超家族 H-superfamily homologous superfamily | 44 — |
| 结构域编号 domain_id | 1k32B04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1k32B05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 226 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 结构域编号 domain_id | 1k32C01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 60 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | 1k32C02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 1k32C03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 750 — Transcription Regulator spoIIAA |
| 同源超家族 H-superfamily homologous superfamily | 44 — |
| 结构域编号 domain_id | 1k32C04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1k32C05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 226 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 结构域编号 domain_id | 1k32D01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 60 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | 1k32D02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 1k32D03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 750 — Transcription Regulator spoIIAA |
| 同源超家族 H-superfamily homologous superfamily | 44 — |
| 结构域编号 domain_id | 1k32D04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1k32D05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 226 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 结构域编号 domain_id | 1k32E01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 60 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | 1k32E02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 1k32E03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 750 — Transcription Regulator spoIIAA |
| 同源超家族 H-superfamily homologous superfamily | 44 — |
| 结构域编号 domain_id | 1k32E04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1k32E05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 226 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 结构域编号 domain_id | 1k32F01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 120 — 6 Propeller |
| 拓扑 Topology topology | 10 — Neuraminidase |
| 同源超家族 H-superfamily homologous superfamily | 60 — Tricorn protease N-terminal domain |
| 结构域编号 domain_id | 1k32F02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 1k32F03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 750 — Transcription Regulator spoIIAA |
| 同源超家族 H-superfamily homologous superfamily | 44 — |
| 结构域编号 domain_id | 1k32F04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 42 — Pdz3 Domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — PDZ domain |
| 结构域编号 domain_id | 1k32F05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 226 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2-enoyl-CoA Hydratase; Chain A, domain 1 |