2cmr
Crystal structure of the HIV-1 neutralizing antibody D5 Fab bound to the gp41 inner-core mimetic 5-helix
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 | 2cmr |
| 沉积日期 deposition_date | 2006-05-11 |
| 结构标题 title | Crystal structure of the HIV-1 neutralizing antibody D5 Fab bound to the gp41 inner-core mimetic 5-helix |
| 关键词 keywords | ;IMMUNE SYSTEM, IMMUNOGLOBULIN COMPLEX, NEUTRALIZATION, IMMUNOGLOBULIN, ENVELOPE PROTEIN, HIV, GP41, AIDS, MHC I, MEMBRANE, TRANSMEMBRANE, IMMUNOGLOBULIN DOMAIN ;; 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 | 31.00 Å |
| 回转半径 Rg (电子) rg_electron | 30.79 Å |
| 零角强度 I(0) i0 | 71701400.00 |
| 分子量 molecular_weight | 66411.0 kDa |
| 排除体积 excluded_volume | 82991 ų |
| 包络体积 envelope_volume | 107770 ų |
| 水化壳体积 shell_volume | 31172 ų |
| 包络直径 envelope_diameter | 111.8 Å |
| 壳层 Rg shell_rg | 35.62 Å |
| 包络 Rg envelope_rg | 30.85 Å |
| 形状 Rg shape_rg | 30.75 Å |
| 总 Rg total_rg | 31.33 Å |
| 总原子数 total_atoms | 4680 |
| 残基数 n_residues | 600 |
| 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 | 106.8 Å |
| Rg (实空间) rg_real | 31.25 Å |
| Rg 误差 (实空间) rg_real_error | 0.98 Å |
| I(0) (实空间) i0_real | 7.1700e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.1970e+06 |
| Rg (倒空间) rg_reciprocal | 31.14 Å |
| I(0) (倒空间) i0_reciprocal | 71700000.0000 |
| 解质量估计 total_estimate | 0.8458 |
| 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 | 33.5 Å |
| 偏度 Skewness skewness | 0.528 |
| 峰度 Kurtosis kurtosis | -0.269 |
| 角度范围 angular_range | — – 0.2550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9758000.0000 |
| 实空间数据点数 n_real_points | 52 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.768; Smooth: 0.895 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d2cmrh_ |
| 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 | d2cmrl1 |
| 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 | d2cmrl2 |
| 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 | 2cmrA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 1860 — |
| 结构域编号 domain_id | 2cmrH01 |
| 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 | 2cmrH02 |
| 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 | 2cmrL01 |
| 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 | 2cmrL02 |
| 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 |