8dzc
Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor 17
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 | 8dzc |
| 沉积日期 deposition_date | 2022-08-06 |
| 结构标题 title | Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor 17 |
| 关键词 keywords | ;COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, coronavirus, main protease, 3CL, MPRO, PRO, GC376, calpain inhibitor II, leupeptin, calpain, aldehyde, GC-376, 3cl-like, a-ketoamide, alpheketoamide, alpha, ketoamide, petidometic, protease, cysteine, HYDROLASE-HYDROLASE INHIBITOR complex, VIRAL PROTEIN-INHIBITOR complex ;; VIRAL PROTEIN/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 | 22.49 Å |
| 回转半径 Rg (电子) rg_electron | 21.80 Å |
| 零角强度 I(0) i0 | 20450700.00 |
| 分子量 molecular_weight | 34113.0 kDa |
| 排除体积 excluded_volume | 42537 ų |
| 包络体积 envelope_volume | 50208 ų |
| 水化壳体积 shell_volume | 20083 ų |
| 包络直径 envelope_diameter | 78.5 Å |
| 壳层 Rg shell_rg | 27.55 Å |
| 包络 Rg envelope_rg | 22.05 Å |
| 形状 Rg shape_rg | 21.79 Å |
| 总 Rg total_rg | 22.60 Å |
| 总原子数 total_atoms | 2390 |
| 残基数 n_residues | 303 |
| 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 | 78.5 Å |
| Rg (实空间) rg_real | 22.59 Å |
| Rg 误差 (实空间) rg_real_error | 0.77 Å |
| I(0) (实空间) i0_real | 2.0450e+07 |
| I(0) 误差 (实空间) i0_real_error | 3.0060e+05 |
| Rg (倒空间) rg_reciprocal | 22.56 Å |
| I(0) (倒空间) i0_reciprocal | 20450000.0000 |
| 解质量估计 total_estimate | 0.5812 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 22.6 Å |
| 偏度 Skewness skewness | 0.479 |
| 峰度 Kurtosis kurtosis | -0.335 |
| 角度范围 angular_range | — – 0.3550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9178000.0000 |
| 实空间数据点数 n_real_points | 67 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.703; Stabil: 0.999; Sysdev: 0.189; Positv: 1.000; Valcen: 0.879; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 2 domains
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 8dzcA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trypsin-like serine proteases |
| 结构域编号 domain_id | 8dzcA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1840 — main proteinase (3clpro) structure, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — main proteinase (3clpro) structure, domain 3 |