1nqt

Crystal structure of bovine Glutamate dehydrogenase-ADP complex

Method: X-RAY DIFFRACTION Dmax: 210.7 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

SAXS profile for 1nqt

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1nqt
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1nqt
沉积日期 deposition_date2003-01-23
结构标题 titleCrystal structure of bovine Glutamate dehydrogenase-ADP complex
关键词 keywordsglutamate dehydrogenase-ADP complex, dimer of two hexamers, regulation, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 methodX-RAY DIFFRACTION

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier69.69
回转半径 Rg (电子) rg_electron70.27
零角强度 I(0) i06320980000.00
分子量 molecular_weight665570.0 kDa
排除体积 excluded_volume830040 ų
包络体积 envelope_volume1154300 ų
水化壳体积 shell_volume139140 ų
包络直径 envelope_diameter251.5
壳层 Rg shell_rg65.71
包络 Rg envelope_rg69.95
形状 Rg shape_rg70.26
总 Rg total_rg70.22
总原子数 total_atoms46812
残基数 n_residues5952
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax210.7
Rg (实空间) rg_real69.50
Rg 误差 (实空间) rg_real_error1.14
I(0) (实空间) i0_real6.2970e+09
I(0) 误差 (实空间) i0_real_error1.1820e+08
Rg (倒空间) rg_reciprocal68.27
I(0) (倒空间) i0_reciprocal6299000000.0000
解质量估计 total_estimate0.5769
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary57.5
偏度 Skewness skewness0.480
峰度 Kurtosis kurtosis-0.588
角度范围 angular_range— – 0.1100 −1
当前正则化参数 α current_alpha0.0347
最高正则化参数 α highest_alpha2230000000.0000
实空间数据点数 n_real_points23
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.825; Stabil: 0.998; Sysdev: 0.006; Positv: 1.000; Valcen: 0.989; Smooth: 0.008

4. 晶体学与实验 4. Crystallography & Experiment

5. 实体与聚合体信息 (2)

6. 折叠分类 (SCOP + CATH) 60 domains

SCOP 2.08 (24 domains)

结构域编号 domain_idd1nqta1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqta2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqtb1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqtb2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqtc1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqtc2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqtd1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqtd2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqte1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqte2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqtf1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqtf2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqtg1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqtg2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqth1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqth2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqti1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqti2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqtj1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqtj2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqtk1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqtk2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases
结构域编号 domain_idd1nqtl1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
结构域编号 domain_idd1nqtl2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
超家族 Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
家族 Family familyc.58.1.1 — Aminoacid dehydrogenases

CATH v4.4 (36 domains)

结构域编号 domain_id1nqtA01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtA02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtA03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtB01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtB02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtB03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtC01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtC02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtC03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtD01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtD02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtD03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtE01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtE02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtE03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtF01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtF02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtF03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtG01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtG02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtG03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtH01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtH02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtH03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtI01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtI02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtI03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtJ01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtJ02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtJ03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtK01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtK02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtK03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140
结构域编号 domain_id1nqtL01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
结构域编号 domain_id1nqtL02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id1nqtL03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily140

7. 引用文献 (1)

8. 文件与曲线 (10)