2adf
;Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody Directed Against the von Willebrand factor A3-Domain ;
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 | 2adf |
| 沉积日期 deposition_date | 2005-07-20 |
| 结构标题 title | ;Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody Directed Against the von Willebrand factor A3-Domain ; |
| 关键词 keywords | on Willebrand factor, A3-domain, 82D6A3, collagen binding, paratope, epitope, antithrombotic, BLOOD CLOTTING-IMMUNE SYSTEM COMPLEX; BLOOD CLOTTING/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 | 30.61 Å |
| 回转半径 Rg (电子) rg_electron | 30.18 Å |
| 零角强度 I(0) i0 | 73665500.00 |
| 分子量 molecular_weight | 67161.0 kDa |
| 排除体积 excluded_volume | 83765 ų |
| 包络体积 envelope_volume | 106240 ų |
| 水化壳体积 shell_volume | 30990 ų |
| 包络直径 envelope_diameter | 106.4 Å |
| 壳层 Rg shell_rg | 35.55 Å |
| 包络 Rg envelope_rg | 30.06 Å |
| 形状 Rg shape_rg | 30.13 Å |
| 总 Rg total_rg | 30.82 Å |
| 总原子数 total_atoms | 4723 |
| 残基数 n_residues | 616 |
| 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 | 102.6 Å |
| Rg (实空间) rg_real | 30.83 Å |
| Rg 误差 (实空间) rg_real_error | 0.86 Å |
| I(0) (实空间) i0_real | 7.3670e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.1340e+06 |
| Rg (倒空间) rg_reciprocal | 30.74 Å |
| I(0) (倒空间) i0_reciprocal | 73660000.0000 |
| 解质量估计 total_estimate | 0.8501 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 29.6 Å |
| 偏度 Skewness skewness | 0.518 |
| 峰度 Kurtosis kurtosis | -0.317 |
| 角度范围 angular_range | — – 0.2600 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 14260000.0000 |
| 实空间数据点数 n_real_points | 53 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.839; Smooth: 0.764 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 9 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2adfa_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.62 — vWA-like |
| 超家族 Superfamily superfamily | c.62.1 — vWA-like |
| 家族 Family family | c.62.1.1 — Integrin A (or I) domain |
| 结构域编号 domain_id | d2adfh_ |
| 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.1.1.0 — automated matches |
| 结构域编号 domain_id | d2adfl1 |
| 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 | d2adfl2 |
| 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) |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 2adfA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 410 — von Willebrand factor, type A domain |
| 结构域编号 domain_id | 2adfH01 |
| 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 | 2adfH02 |
| 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 | 2adfL01 |
| 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 | 2adfL02 |
| 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 |