1lwu

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide

Method: X-RAY DIFFRACTION Dmax: 285.4 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1lwu

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id1lwu
沉积日期 deposition_date2002-06-03
结构标题 titleCrystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide
关键词 keywordsheterotrimer, protein-peptide complex, BLOOD CLOTTING; BLOOD CLOTTING
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_guinier
回转半径 Rg (电子) rg_electron114.40
零角强度 I(0) i01833040000.00
分子量 molecular_weight346400.0 kDa
排除体积 excluded_volume427110 ų
包络体积 envelope_volume849380 ų
水化壳体积 shell_volume83471 ų
包络直径 envelope_diameter448.3
壳层 Rg shell_rg60.31
包络 Rg envelope_rg115.70
形状 Rg shape_rg114.50
总 Rg total_rg113.10
总原子数 total_atoms24360
残基数 n_residues2932
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 dmax285.4
Rg (实空间) rg_real97.24
Rg 误差 (实空间) rg_real_error1.78
I(0) (实空间) i0_real1.7310e+09
I(0) 误差 (实空间) i0_real_error3.6990e+07
Rg (倒空间) rg_reciprocal90.81
I(0) (倒空间) i0_reciprocal1731000000.0000
解质量估计 total_estimate0.7832
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary40.8
偏度 Skewness skewness0.284
峰度 Kurtosis kurtosis-0.993
角度范围 angular_range— – 0.0700 −1
当前正则化参数 α current_alpha0.3314
最高正则化参数 α highest_alpha34310000.0000
实空间数据点数 n_real_points15
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.042; Oscil: 0.604; Stabil: 0.982; Sysdev: 1.000; Positv: 1.000; Valcen: 0.576; Smooth: 0.000

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

5. 实体与聚合体信息 (11)

6. 折叠分类 (SCOP + CATH) 48 domains

SCOP 2.08 (20 domains)

结构域编号 domain_idd1lwua_
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwub1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
家族 Family familyd.171.1.1 — Fibrinogen C-terminal domain-like
结构域编号 domain_idd1lwub2
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwuc1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
家族 Family familyd.171.1.1 — Fibrinogen C-terminal domain-like
结构域编号 domain_idd1lwuc2
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwud_
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwue1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
家族 Family familyd.171.1.1 — Fibrinogen C-terminal domain-like
结构域编号 domain_idd1lwue2
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwuf1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
家族 Family familyd.171.1.1 — Fibrinogen C-terminal domain-like
结构域编号 domain_idd1lwuf2
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwug_
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwuh1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
家族 Family familyd.171.1.1 — Fibrinogen C-terminal domain-like
结构域编号 domain_idd1lwuh2
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwui1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
家族 Family familyd.171.1.1 — Fibrinogen C-terminal domain-like
结构域编号 domain_idd1lwui2
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwuj_
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwuk1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
家族 Family familyd.171.1.1 — Fibrinogen C-terminal domain-like
结构域编号 domain_idd1lwuk2
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions
结构域编号 domain_idd1lwul1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.171 — Fibrinogen C-terminal domain-like
超家族 Superfamily superfamilyd.171.1 — Fibrinogen C-terminal domain-like
家族 Family familyd.171.1.1 — Fibrinogen C-terminal domain-like
结构域编号 domain_idd1lwul2
类 Class classh — Coiled coil proteins
折叠类型 Fold foldh.1 — Parallel coiled-coil
超家族 Superfamily superfamilyh.1.8 — Fibrinogen coiled-coil and central regions
家族 Family familyh.1.8.1 — Fibrinogen coiled-coil and central regions

CATH v4.4 (28 domains)

结构域编号 domain_id1lwuA00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuB01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
结构域编号 domain_id1lwuB02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
结构域编号 domain_id1lwuB03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuC01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
结构域编号 domain_id1lwuC02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
结构域编号 domain_id1lwuC03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuD00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuE01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
结构域编号 domain_id1lwuE02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
结构域编号 domain_id1lwuE03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuF01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
结构域编号 domain_id1lwuF02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
结构域编号 domain_id1lwuF03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuG00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuH01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
结构域编号 domain_id1lwuH02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
结构域编号 domain_id1lwuH03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuI01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
结构域编号 domain_id1lwuI02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
结构域编号 domain_id1lwuI03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuJ00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuK01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
结构域编号 domain_id1lwuK02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
结构域编号 domain_id1lwuK03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50
结构域编号 domain_id1lwuL01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
结构域编号 domain_id1lwuL02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
结构域编号 domain_id1lwuL03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily50

7. 引用文献 (1)

8. 文件与曲线 (10)