2qjp

Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited

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

Cytochrome b

Rhodobacter sphaeroides

UniProt Q02761

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 6 Cytochrome c1 × 2 (Q3IY11) Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 (Q02762) 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 6 Cytochrome c1 × 2 (Q3IY11) Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 (Q02762) 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6 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 CYB_RHOSH
Isoform —
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–428; UniProt 3–430 作者链 D; PDB构建体 1–428; UniProt 3–430 作者链 G; PDB构建体 1–428; UniProt 3–430 作者链 J; PDB构建体 1–428; UniProt 3–430

Cytochrome c1

Rhodobacter sphaeroides

UniProt Q3IY11

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 6 Cytochrome b × 2 (Q02761) Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 (Q02762) 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 6 Cytochrome b × 2 (Q02761) Ubiquinol-cytochrome c reductase iron-sulfur subunit × 2 (Q02762) 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6 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 Q3IY11_RHOS4
Isoform —
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–256; UniProt 23–278 作者链 E; PDB构建体 1–256; UniProt 23–278 作者链 H; PDB构建体 1–256; UniProt 23–278 作者链 K; PDB构建体 1–256; UniProt 23–278

Ubiquinol-cytochrome c reductase iron-sulfur subunit

Rhodobacter sphaeroides

UniProt Q02762

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 6 Cytochrome b × 2 (Q02761) Cytochrome c1 × 2 (Q3IY11) 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 2 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 6 Cytochrome b × 2 (Q02761) Cytochrome c1 × 2 (Q3IY11) 2-O-octyl-beta-D-glucopyranose × 2 PROTOPORPHYRIN IX CONTAINING FE × 6 STIGMATELLIN A × 2 (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE × 2 ;(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE ; × 2 STRONTIUM ION × 4 FE2/S2 (INORGANIC) CLUSTER × 2 water × 6 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 UCRI_RHOSH
Isoform —
PDB实体 3
链与序列区间 作者链 C; PDB构建体 1–179; UniProt 9–187 作者链 F; PDB构建体 1–179; UniProt 9–187 作者链 I; PDB构建体 1–179; UniProt 9–187 作者链 L; PDB构建体 1–179; UniProt 9–187

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_id2qjp
沉积日期 deposition_date2007-07-08
结构标题 titleCrystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited
关键词 keywords;Cytochrome b with 8 TM helices, one c-term TM in cytochrome c1 and an N-term TM in the iron-sulfur-protein (Rieske), Electron transport, Heme, Membrane, Metal-binding, Respiratory chain, Transmembrane, Transport, 2Fe-2S, Inner membrane, Oxidoreductase ;; ELECTRON TRANSPORT
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。

2qjp__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

2qjp__assembly_2__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。

2qjp__assembly_2__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)38.68 Å
Rg(电子密度)37.31 Å
总 Rg37.87 Å
原子数14010
残基数1726
排除体积252640 ų
最大 q0.500 Å⁻¹
Assembly Model 结构单元 聚集说明 状态 CRYSOL 操作
1 1 2qjp__assembly_1__model_1 hexameric (6) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
2 1 2qjp__assembly_2__model_1 hexameric (6) 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 (11)

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6. 折叠分类 (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

结构域编号 domain_id2qjpA00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology810 — Cytochrome Bc1 Complex; Chain C
同源超家族 H-superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
结构域编号 domain_id2qjpB01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c-like domain
结构域编号 domain_id2qjpB02
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 superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
结构域编号 domain_id2qjpC01
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 superfamily510 — Single helix bin
结构域编号 domain_id2qjpC02
类 Class class2 — Mainly Beta
架构 Architecture architecture102 — 3-layer Sandwich
拓扑 Topology topology10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
结构域编号 domain_id2qjpD00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology810 — Cytochrome Bc1 Complex; Chain C
同源超家族 H-superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
结构域编号 domain_id2qjpE01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c-like domain
结构域编号 domain_id2qjpE02
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 superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
结构域编号 domain_id2qjpF01
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 superfamily510 — Single helix bin
结构域编号 domain_id2qjpF02
类 Class class2 — Mainly Beta
架构 Architecture architecture102 — 3-layer Sandwich
拓扑 Topology topology10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
结构域编号 domain_id2qjpG00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology810 — Cytochrome Bc1 Complex; Chain C
同源超家族 H-superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
结构域编号 domain_id2qjpH01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c-like domain
结构域编号 domain_id2qjpH02
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 superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
结构域编号 domain_id2qjpI01
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 superfamily510 — Single helix bin
结构域编号 domain_id2qjpI02
类 Class class2 — Mainly Beta
架构 Architecture architecture102 — 3-layer Sandwich
拓扑 Topology topology10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
结构域编号 domain_id2qjpJ00
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology810 — Cytochrome Bc1 Complex; Chain C
同源超家族 H-superfamily homologous superfamily10 — Cytochrome Bc1 Complex; Chain C
结构域编号 domain_id2qjpK01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily10 — Cytochrome c-like domain
结构域编号 domain_id2qjpK02
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 superfamily100 — Cytochrome c1, transmembrane anchor, C-terminal
结构域编号 domain_id2qjpL01
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 superfamily510 — Single helix bin
结构域编号 domain_id2qjpL02
类 Class class2 — Mainly Beta
架构 Architecture architecture102 — 3-layer Sandwich
拓扑 Topology topology10 — Rieske Iron-sulfur Protein
同源超家族 H-superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
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7. 引用文献 (1)