1yyl
;crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b ;
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 | 1yyl |
| 沉积日期 deposition_date | 2005-02-25 |
| 结构标题 title | ;crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b ; |
| 关键词 keywords | HIV-1, gp120, YU2, scorpion toxin, CD4 mimic, CD4M33, antibody, Viral protein-Immune system COMPLEX; Viral protein/Immune system |
| 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 | 45.00 Å |
| 回转半径 Rg (电子) rg_electron | 44.76 Å |
| 零角强度 I(0) i0 | 454915000.00 |
| 分子量 molecular_weight | 171670.0 kDa |
| 排除体积 excluded_volume | 213630 ų |
| 包络体积 envelope_volume | 310980 ų |
| 水化壳体积 shell_volume | 59617 ų |
| 包络直径 envelope_diameter | 175.9 Å |
| 壳层 Rg shell_rg | 47.37 Å |
| 包络 Rg envelope_rg | 44.13 Å |
| 形状 Rg shape_rg | 44.72 Å |
| 总 Rg total_rg | 45.02 Å |
| 总原子数 total_atoms | 12046 |
| 残基数 n_residues | 1502 |
| 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 | 154.6 Å |
| Rg (实空间) rg_real | 44.89 Å |
| Rg 误差 (实空间) rg_real_error | 1.82 Å |
| I(0) (实空间) i0_real | 4.5490e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.7630e+06 |
| Rg (倒空间) rg_reciprocal | 45.00 Å |
| I(0) (倒空间) i0_reciprocal | 455000000.0000 |
| 解质量估计 total_estimate | 0.8090 |
| 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 | 61.9 Å |
| 偏度 Skewness skewness | 0.127 |
| 峰度 Kurtosis kurtosis | -0.589 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 37910000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 22 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1yylg_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.172 — gp120 core |
| 超家族 Superfamily superfamily | d.172.1 — gp120 core |
| 家族 Family family | d.172.1.1 — gp120 core |
| 结构域编号 domain_id | d1yylh1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.1 — V set domains (antibody variable domain-like) |
| 结构域编号 domain_id | d1yylh2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.2 — C1 set domains (antibody constant domain-like) |
| 结构域编号 domain_id | d1yyll1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.1 — V set domains (antibody variable domain-like) |
| 结构域编号 domain_id | d1yyll2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.2 — C1 set domains (antibody constant domain-like) |
| 结构域编号 domain_id | d1yylm1 |
| 类 Class class | k — Designed proteins |
| 折叠类型 Fold fold | k.23 — Scorpion toxin-based designs |
| 超家族 Superfamily superfamily | k.23.1 — Scorpion toxin-based designs |
| 家族 Family family | k.23.1.2 — Mini-protein reproducing the core of the CD4 surface |
| 结构域编号 domain_id | d1yylp_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.172 — gp120 core |
| 超家族 Superfamily superfamily | d.172.1 — gp120 core |
| 家族 Family family | d.172.1.1 — gp120 core |
| 结构域编号 domain_id | d1yylq1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.1 — V set domains (antibody variable domain-like) |
| 结构域编号 domain_id | d1yylq2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.2 — C1 set domains (antibody constant domain-like) |
| 结构域编号 domain_id | d1yylr1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.1 — V set domains (antibody variable domain-like) |
| 结构域编号 domain_id | d1yylr2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.1 — Immunoglobulin |
| 家族 Family family | b.1.1.2 — C1 set domains (antibody constant domain-like) |
| 结构域编号 domain_id | d1yyls1 |
| 类 Class class | k — Designed proteins |
| 折叠类型 Fold fold | k.23 — Scorpion toxin-based designs |
| 超家族 Superfamily superfamily | k.23.1 — Scorpion toxin-based designs |
| 家族 Family family | k.23.1.2 — Mini-protein reproducing the core of the CD4 surface |
CATH v4.4 (10 domains)
| 结构域编号 domain_id | 1yylG00 |
| 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 | 1yylH01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1yylH02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1yylL01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1yylL02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1yylP00 |
| 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 | 1yylQ01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1yylQ02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1yylR01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1yylR02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |