8fm5
HIV-1 gp120 complex with DY-III-065
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 | 8fm5 |
| 沉积日期 deposition_date | 2022-12-22 |
| 结构标题 title | HIV-1 gp120 complex with DY-III-065 |
| 关键词 keywords | ;retrovirus, gp120, entry inhibitor, structure-based drug design, small molecule, antiretroviral therapy, 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 | 40.03 Å |
| 回转半径 Rg (电子) rg_electron | 39.76 Å |
| 零角强度 I(0) i0 | 398668000.00 |
| 分子量 molecular_weight | 157560.0 kDa |
| 排除体积 excluded_volume | 194790 ų |
| 包络体积 envelope_volume | 260790 ų |
| 水化壳体积 shell_volume | 54888 ų |
| 包络直径 envelope_diameter | 127.8 Å |
| 壳层 Rg shell_rg | 45.27 Å |
| 包络 Rg envelope_rg | 39.05 Å |
| 形状 Rg shape_rg | 39.73 Å |
| 总 Rg total_rg | 40.12 Å |
| 总原子数 total_atoms | 11032 |
| 残基数 n_residues | 1340 |
| 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 | 126.0 Å |
| Rg (实空间) rg_real | 39.93 Å |
| Rg 误差 (实空间) rg_real_error | 1.22 Å |
| I(0) (实空间) i0_real | 3.9870e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.1370e+06 |
| Rg (倒空间) rg_reciprocal | 40.03 Å |
| I(0) (倒空间) i0_reciprocal | 398700000.0000 |
| 解质量估计 total_estimate | 0.9077 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 45.2 Å |
| 偏度 Skewness skewness | 0.118 |
| 峰度 Kurtosis kurtosis | -0.748 |
| 角度范围 angular_range | — – 0.1950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 43620000.0000 |
| 实空间数据点数 n_real_points | 40 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.936 |
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) 4 domains
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 8fm5A01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 40 — HIV Envelope Protein Gp120; Chain G |
| 同源超家族 H-superfamily homologous superfamily | 20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein |
| 结构域编号 domain_id | 8fm5B01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 40 — HIV Envelope Protein Gp120; Chain G |
| 同源超家族 H-superfamily homologous superfamily | 20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein |
| 结构域编号 domain_id | 8fm5C01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 40 — HIV Envelope Protein Gp120; Chain G |
| 同源超家族 H-superfamily homologous superfamily | 20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein |
| 结构域编号 domain_id | 8fm5D01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 40 — HIV Envelope Protein Gp120; Chain G |
| 同源超家族 H-superfamily homologous superfamily | 20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein |