2g50
The location of the allosteric amino acid binding site of muscle pyruvate kinase.
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 | 2g50 |
| 沉积日期 deposition_date | 2006-02-22 |
| 结构标题 title | The location of the allosteric amino acid binding site of muscle pyruvate kinase. |
| 关键词 keywords | allostery, pyruvate kinase, glycolysis, kinase, phosphoryl transfer, TRANSFERASE; TRANSFERASE |
| 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 | 56.71 Å |
| 回转半径 Rg (电子) rg_electron | 56.93 Å |
| 零角强度 I(0) i0 | 2987760000.00 |
| 分子量 molecular_weight | 459650.0 kDa |
| 排除体积 excluded_volume | 576290 ų |
| 包络体积 envelope_volume | 768690 ų |
| 水化壳体积 shell_volume | 111330 ų |
| 包络直径 envelope_diameter | 198.4 Å |
| 壳层 Rg shell_rg | 59.83 Å |
| 包络 Rg envelope_rg | 56.23 Å |
| 形状 Rg shape_rg | 56.94 Å |
| 总 Rg total_rg | 56.98 Å |
| 总原子数 total_atoms | 32124 |
| 残基数 n_residues | 4128 |
| 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 | 195.5 Å |
| Rg (实空间) rg_real | 56.76 Å |
| Rg 误差 (实空间) rg_real_error | 1.67 Å |
| I(0) (实空间) i0_real | 2.9880e+09 |
| I(0) 误差 (实空间) i0_real_error | 6.2050e+07 |
| Rg (倒空间) rg_reciprocal | 56.64 Å |
| I(0) (倒空间) i0_reciprocal | 2987000000.0000 |
| 解质量估计 total_estimate | 0.8792 |
| 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 | 62.8 Å |
| 偏度 Skewness skewness | 0.324 |
| 峰度 Kurtosis kurtosis | -0.521 |
| 角度范围 angular_range | — – 0.1400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0002 |
| 最高正则化参数 α highest_alpha | 258500000.0000 |
| 实空间数据点数 n_real_points | 29 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.880 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (10)
6. 折叠分类 (SCOP + CATH) 48 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d2g50a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d2g50a2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d2g50a3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d2g50b1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d2g50b2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d2g50b3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d2g50c1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d2g50c2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d2g50c3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d2g50d1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d2g50d2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d2g50d3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d2g50e1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d2g50e2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d2g50e3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d2g50f1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d2g50f2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d2g50f3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d2g50g1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d2g50g2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d2g50g3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d2g50h1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d2g50h2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d2g50h3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 2g50A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 2g50A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 2g50A03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 2g50B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 2g50B02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 2g50B03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 2g50C01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 2g50C02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 2g50C03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 2g50D01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 2g50D02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 2g50D03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 2g50E01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 2g50E02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 2g50E03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 2g50F01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 2g50F02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 2g50F03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 2g50G01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 2g50G02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 2g50G03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 2g50H01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 2g50H02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 2g50H03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |