1g65

;Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity of alpha,beta-epoxyketone proteasome inhibitors ;

Method: X-RAY DIFFRACTION Dmax: 189.0 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1g65

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1g65
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1g65
沉积日期 deposition_date2000-11-03
结构标题 title;Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity of alpha,beta-epoxyketone proteasome inhibitors ;
关键词 keywordsproteasome, epoxomicin, ubiquitin, ntn-hydolase, protease, HYDROLASE-HYDROLASE inhibitor complex; HYDROLASE/HYDROLASE inhibitor
实验方法 methodX-RAY DIFFRACTION

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier60.27
回转半径 Rg (电子) rg_electron59.79
零角强度 I(0) i013839600000.00
分子量 molecular_weight654840.0 kDa
排除体积 excluded_volume631670 ų
包络体积 envelope_volume1263900 ų
水化壳体积 shell_volume169350 ų
包络直径 envelope_diameter197.9
壳层 Rg shell_rg68.01
包络 Rg envelope_rg57.74
形状 Rg shape_rg59.79
总 Rg total_rg59.91
总原子数 total_atoms49636
残基数 n_residues6372
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax189.0
Rg (实空间) rg_real59.98
Rg 误差 (实空间) rg_real_error1.19
I(0) (实空间) i0_real1.3840e+10
I(0) 误差 (实空间) i0_real_error2.6150e+08
Rg (倒空间) rg_reciprocal60.50
I(0) (倒空间) i0_reciprocal13850000000.0000
解质量估计 total_estimate0.8430
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary80.0
偏度 Skewness skewness0.204
峰度 Kurtosis kurtosis-0.419
角度范围 angular_range— – 0.1300 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha992600000.0000
实空间数据点数 n_real_points27
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.444

4. 晶体学与实验 4. Crystallography & Experiment

5. 实体与聚合体信息 (17)

6. 折叠分类 (SCOP + CATH) 56 domains

SCOP 2.08 (28 domains)

结构域编号 domain_idd1g651_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g652_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65a_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65b_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65c_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65d_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65e_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65f_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65g_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65h_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65i_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65j_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65k_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65l_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65m_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65n_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65o_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65p_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65q_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65r_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65s_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65t_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65u_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65v_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65w_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65x_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65y_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits
结构域编号 domain_idd1g65z_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.153 — Ntn hydrolase-like
超家族 Superfamily superfamilyd.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family familyd.153.1.4 — Proteasome subunits

CATH v4.4 (28 domains)

结构域编号 domain_id1g65100
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65200
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65A00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65B00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65C00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65D00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65E00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65F00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65G00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65H00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65I00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65J00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65K00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65L00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65M00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65N00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65O00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65P00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65Q00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65R00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65S00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65T00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65U00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65V00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65W00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65X00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65Y00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain
结构域编号 domain_id1g65Z00
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

7. 引用文献 (1)

8. 文件与曲线 (10)