2hod

Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide

Method: X-RAY DIFFRACTION
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Fibrinogen alpha chain

物种未注明

UniProt P02671

当前结构中的状态

Assembly 物理组成 蛋白状态 分子拷贝数 共同组分 数据核对
1 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen beta chain × 1 (P02675) Fibrinogen, gamma polypeptide × 1 (Q53Y18) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen beta chain × 1 (P02675) Fibrinogen, gamma polypeptide × 1 (Q53Y18) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen beta chain × 1 (P02675) Fibrinogen, gamma polypeptide × 1 (Q53Y18) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen beta chain × 1 (P02675) Fibrinogen, gamma polypeptide × 1 (Q53Y18) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3 与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据
UniProt名称 FIBA_HUMAN
Isoform —
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–87; UniProt 130–216 作者链 D; PDB构建体 1–87; UniProt 130–216 作者链 G; PDB构建体 1–87; UniProt 130–216 作者链 J; PDB构建体 1–87; UniProt 130–216

Fibrinogen beta chain

物种未注明

UniProt P02675

当前结构中的状态

Assembly 物理组成 蛋白状态 分子拷贝数 共同组分 数据核对
1 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen alpha chain × 1 (P02671) Fibrinogen, gamma polypeptide × 1 (Q53Y18) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen alpha chain × 1 (P02671) Fibrinogen, gamma polypeptide × 1 (Q53Y18) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen alpha chain × 1 (P02671) Fibrinogen, gamma polypeptide × 1 (Q53Y18) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen alpha chain × 1 (P02671) Fibrinogen, gamma polypeptide × 1 (Q53Y18) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3 与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据
UniProt名称 FIBB_HUMAN
Isoform —
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–328; UniProt 164–491 作者链 E; PDB构建体 1–328; UniProt 164–491 作者链 H; PDB构建体 1–328; UniProt 164–491 作者链 K; PDB构建体 1–328; UniProt 164–491

Fibrinogen, gamma polypeptide

物种未注明

UniProt Q53Y18

当前结构中的状态

Assembly 物理组成 蛋白状态 分子拷贝数 共同组分 数据核对
1 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen alpha chain × 1 (P02671) Fibrinogen beta chain × 1 (P02675) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen alpha chain × 1 (P02671) Fibrinogen beta chain × 1 (P02675) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen alpha chain × 1 (P02671) Fibrinogen beta chain × 1 (P02675) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 5 Fibrinogen alpha chain × 1 (P02671) Fibrinogen beta chain × 1 (P02675) Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3 与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据
UniProt名称 Q53Y18_HUMAN
Isoform —
PDB实体 3
链与序列区间 作者链 C; PDB构建体 1–323; UniProt 115–437 作者链 F; PDB构建体 1–323; UniProt 115–437 作者链 I; PDB构建体 1–323; UniProt 115–437 作者链 L; PDB构建体 1–323; UniProt 115–437

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中;数据库内部编号、导入时间和 assembly 操作表达式仅用于维护,因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id2hod
沉积日期 deposition_date2006-07-14
结构标题 titleCrystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide
关键词 keywordsKnob-hole interactions, BLOOD CLOTTING-PEPTIDE complex; BLOOD CLOTTING/PEPTIDE
实验方法 methodX-RAY DIFFRACTION
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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

2hod__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

2hod__assembly_4__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 个绘图点;横轴和纵轴均采用对数尺度。

2hod__assembly_4__model_1 | P(r) · Pending

新版 assembly/model P(r) 尚未计算 此处仅保留位置,不展示旧数据 r (Angstrom) P(r)
P(r) 将按相同 assembly/model 分别计算和展示。
Rg(Guinier)34.55 Å
Rg(电子密度)35.32 Å
总 Rg35.46 Å
原子数5583
残基数690
排除体积98213 ų
最大 q0.500 Å⁻¹
Assembly Model 结构单元 聚集说明 状态 CRYSOL 操作
1 1 2hod__assembly_1__model_1 pentameric (5) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
2 1 2hod__assembly_2__model_1 pentameric (5) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
3 1 2hod__assembly_3__model_1 pentameric (5) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
4 1 2hod__assembly_4__model_1 pentameric (5) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (6)

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6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (4 domains)

结构域编号 domain_idd2hoda1
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_idd2hodd1
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_idd2hodg1
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_idd2hodj1
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 (24 domains)

结构域编号 domain_id2hodA00
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_id2hodB01
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_id2hodB02
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_id2hodB03
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_id2hodC01
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_id2hodC02
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_id2hodD00
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_id2hodE01
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_id2hodE02
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_id2hodE03
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_id2hodF01
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_id2hodF02
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_id2hodG00
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_id2hodH01
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_id2hodH02
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_id2hodH03
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_id2hodI01
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_id2hodI02
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_id2hodJ00
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_id2hodK01
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_id2hodK02
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_id2hodK03
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_id2hodL01
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_id2hodL02
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
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