2frv

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

Method: X-RAY DIFFRACTION

1. 蛋白身份与相关结构 Protein Identity & Related Structures

PERIPLASMIC HYDROGENASE

物种未注明

UniProt P12943

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 2 PERIPLASMIC HYDROGENASE × 1 (P12944) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12944) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12944) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12944) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
5 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12944) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
6 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12944) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 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 PHNS_DESGI
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–264; UniProt 25–288 作者链 C; PDB构建体 1–264; UniProt 25–288 作者链 E; PDB构建体 1–264; UniProt 25–288 作者链 G; PDB构建体 1–264; UniProt 25–288 作者链 I; PDB构建体 1–264; UniProt 25–288 作者链 S; PDB构建体 1–264; UniProt 25–288

PERIPLASMIC HYDROGENASE

物种未注明

UniProt P12944

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 2 PERIPLASMIC HYDROGENASE × 1 (P12943) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12943) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
3 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12943) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
4 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12943) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
5 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12943) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 与蛋白数一致
6 蛋白异源复合物 异源复合物 蛋白 2 PERIPLASMIC HYDROGENASE × 1 (P12943) IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 OXYGEN ATOM × 1 water × 2 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 PHNL_DESGI
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 2–536; UniProt 1–535 作者链 D; PDB构建体 2–536; UniProt 1–535 作者链 F; PDB构建体 2–536; UniProt 1–535 作者链 H; PDB构建体 2–536; UniProt 1–535 作者链 J; PDB构建体 2–536; UniProt 1–535 作者链 L; PDB构建体 2–536; UniProt 1–535

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。

2. 结构基本信息 2. Structure Basics

条目编号 entry_id2frv
沉积日期 deposition_date1997-06-10
结构标题 titleCRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
关键词 keywordsOXIDOREDUCTASE, NI-FE HYDROGENASE; OXIDOREDUCTASE
实验方法 methodX-RAY DIFFRACTION

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。

2frv__assembly_1__model_1

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

下载该曲线 .dat

2frv__assembly_1__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。

2frv__assembly_1__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)25.55 Å
Rg(电子密度)24.63 Å
总 Rg25.42 Å
原子数6149
残基数791
排除体积109680 ų
最大 q0.500 Å⁻¹
Assembly Model 结构单元 聚集说明 状态 CRYSOL 操作
1 1 2frv__assembly_1__model_1 dimeric (2) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
2 1 2frv__assembly_2__model_1 dimeric (2) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
3 1 2frv__assembly_3__model_1 dimeric (2) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
4 1 2frv__assembly_4__model_1 dimeric (2) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
5 1 2frv__assembly_5__model_1 dimeric (2) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
6 1 2frv__assembly_6__model_1 dimeric (2) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载

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

5. 实体与聚合物信息 Entities & Polymers (9)

6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

结构域编号 domain_idd2frva_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.19 — HydA/Nqo6-like
超家族 Superfamily superfamilye.19.1 — HydA/Nqo6-like
家族 Family familye.19.1.1 — Nickel-iron hydrogenase, small subunit
结构域编号 domain_idd2frvb_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.18 — HydB/Nqo4-like
超家族 Superfamily superfamilye.18.1 — HydB/Nqo4-like
家族 Family familye.18.1.1 — Nickel-iron hydrogenase, large subunit
结构域编号 domain_idd2frvc_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.19 — HydA/Nqo6-like
超家族 Superfamily superfamilye.19.1 — HydA/Nqo6-like
家族 Family familye.19.1.1 — Nickel-iron hydrogenase, small subunit
结构域编号 domain_idd2frvd_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.18 — HydB/Nqo4-like
超家族 Superfamily superfamilye.18.1 — HydB/Nqo4-like
家族 Family familye.18.1.1 — Nickel-iron hydrogenase, large subunit
结构域编号 domain_idd2frve_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.19 — HydA/Nqo6-like
超家族 Superfamily superfamilye.19.1 — HydA/Nqo6-like
家族 Family familye.19.1.1 — Nickel-iron hydrogenase, small subunit
结构域编号 domain_idd2frvf_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.18 — HydB/Nqo4-like
超家族 Superfamily superfamilye.18.1 — HydB/Nqo4-like
家族 Family familye.18.1.1 — Nickel-iron hydrogenase, large subunit
结构域编号 domain_idd2frvg_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.19 — HydA/Nqo6-like
超家族 Superfamily superfamilye.19.1 — HydA/Nqo6-like
家族 Family familye.19.1.1 — Nickel-iron hydrogenase, small subunit
结构域编号 domain_idd2frvh_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.18 — HydB/Nqo4-like
超家族 Superfamily superfamilye.18.1 — HydB/Nqo4-like
家族 Family familye.18.1.1 — Nickel-iron hydrogenase, large subunit
结构域编号 domain_idd2frvi_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.19 — HydA/Nqo6-like
超家族 Superfamily superfamilye.19.1 — HydA/Nqo6-like
家族 Family familye.19.1.1 — Nickel-iron hydrogenase, small subunit
结构域编号 domain_idd2frvj_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.18 — HydB/Nqo4-like
超家族 Superfamily superfamilye.18.1 — HydB/Nqo4-like
家族 Family familye.18.1.1 — Nickel-iron hydrogenase, large subunit
结构域编号 domain_idd2frvl_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.18 — HydB/Nqo4-like
超家族 Superfamily superfamilye.18.1 — HydB/Nqo4-like
家族 Family familye.18.1.1 — Nickel-iron hydrogenase, large subunit
结构域编号 domain_idd2frvs_
类 Class classe — Multi-domain proteins (alpha and beta)
折叠类型 Fold folde.19 — HydA/Nqo6-like
超家族 Superfamily superfamilye.19.1 — HydA/Nqo6-like
家族 Family familye.19.1.1 — Nickel-iron hydrogenase, small subunit

CATH v4.4 (18 domains)

结构域编号 domain_id2frvA01
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 superfamily700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit
结构域编号 domain_id2frvA02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 hydrogenase, C-terminal domain
结构域编号 domain_id2frvB00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 Hydrogenase, chain B
结构域编号 domain_id2frvC01
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 superfamily700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit
结构域编号 domain_id2frvC02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 hydrogenase, C-terminal domain
结构域编号 domain_id2frvD00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 Hydrogenase, chain B
结构域编号 domain_id2frvE01
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 superfamily700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit
结构域编号 domain_id2frvE02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 hydrogenase, C-terminal domain
结构域编号 domain_id2frvF00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 Hydrogenase, chain B
结构域编号 domain_id2frvG01
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 superfamily700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit
结构域编号 domain_id2frvG02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 hydrogenase, C-terminal domain
结构域编号 domain_id2frvH00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 Hydrogenase, chain B
结构域编号 domain_id2frvI01
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 superfamily700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit
结构域编号 domain_id2frvI02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 hydrogenase, C-terminal domain
结构域编号 domain_id2frvJ00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 Hydrogenase, chain B
结构域编号 domain_id2frvL00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology645 — Cytochrome-c3 Hydrogenase; chain B
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 Hydrogenase, chain B
结构域编号 domain_id2frvS01
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 superfamily700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit
结构域编号 domain_id2frvS02
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome-c3 hydrogenase, C-terminal domain

7. 引用文献 (3)