3dva

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

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

Pyruvate dehydrogenase E1 component subunit alpha

Bacillus stearothermophilus

UniProt P21873

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 Pyruvate dehydrogenase E1 component subunit beta × 2 (P21874) Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 (P11961) MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 POTASSIUM ION × 2 water × 5 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 5 Pyruvate dehydrogenase E1 component subunit beta × 2 (P21874) Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 (P11961) MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 water × 5 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 ODPA_BACST
Isoform —
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–369; UniProt 1–369 作者链 C; PDB构建体 1–369; UniProt 1–369 作者链 E; PDB构建体 1–369; UniProt 1–369 作者链 G; PDB构建体 1–369; UniProt 1–369

Pyruvate dehydrogenase E1 component subunit beta

Bacillus stearothermophilus

UniProt P21874

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 Pyruvate dehydrogenase E1 component subunit alpha × 2 (P21873) Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 (P11961) MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 POTASSIUM ION × 2 water × 5 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 5 Pyruvate dehydrogenase E1 component subunit alpha × 2 (P21873) Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 (P11961) MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 water × 5 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 ODPB_BACST
Isoform —
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–325; UniProt 1–325 作者链 D; PDB构建体 1–325; UniProt 1–325 作者链 F; PDB构建体 1–325; UniProt 1–325 作者链 H; PDB构建体 1–325; UniProt 1–325

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

Bacillus stearothermophilus

UniProt P11961

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 Pyruvate dehydrogenase E1 component subunit alpha × 2 (P21873) Pyruvate dehydrogenase E1 component subunit beta × 2 (P21874) MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 POTASSIUM ION × 2 water × 5 与蛋白数一致
2 蛋白异源复合物 异源复合物 蛋白 5 Pyruvate dehydrogenase E1 component subunit alpha × 2 (P21873) Pyruvate dehydrogenase E1 component subunit beta × 2 (P21874) MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 water × 5 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 ODP2_BACST
Isoform —
PDB实体 3
链与序列区间 作者链 I; PDB构建体 1–428; UniProt 1–428 作者链 J; PDB构建体 1–428; UniProt 1–428

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_id3dva
沉积日期 deposition_date2008-07-18
结构标题 titleSnapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
关键词 keywords;Oxidoreductase, PYRUVATE, DEHYDROGENASE, DIHYDROLIPOYL, ACETYL TRANSFERASE, MULTIENZYME COMPLEX, TRANSFERASE, Glycolysis, Phosphoprotein, Thiamine pyrophosphate, Acyltransferase, OXIDOREDUCTASE-TRANSFERASE COMPLEX ;; OXIDOREDUCTASE/TRANSFERASE
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。

3dva__assembly_1__model_1

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

下载该曲线 .dat

3dva__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。

3dva__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)33.30 Å
Rg(电子密度)32.31 Å
总 Rg32.98 Å
原子数11137
残基数1420
排除体积199010 ų
最大 q0.500 Å⁻¹
Assembly Model 结构单元 聚集说明 状态 CRYSOL 操作
1 1 3dva__assembly_1__model_1 pentameric (5) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
2 1 3dva__assembly_2__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 (7)

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6. 折叠分类 (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

结构域编号 domain_idd3dvaa_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family familyc.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module
结构域编号 domain_idd3dvab1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family familyc.36.1.0 — automated matches
结构域编号 domain_idd3dvab2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.48 — TK C-terminal domain-like
超家族 Superfamily superfamilyc.48.1 — TK C-terminal domain-like
家族 Family familyc.48.1.0 — automated matches
结构域编号 domain_idd3dvac_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family familyc.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module
结构域编号 domain_idd3dvad1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family familyc.36.1.0 — automated matches
结构域编号 domain_idd3dvad2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.48 — TK C-terminal domain-like
超家族 Superfamily superfamilyc.48.1 — TK C-terminal domain-like
家族 Family familyc.48.1.0 — automated matches
结构域编号 domain_idd3dvae_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family familyc.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module
结构域编号 domain_idd3dvaf1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family familyc.36.1.0 — automated matches
结构域编号 domain_idd3dvaf2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.48 — TK C-terminal domain-like
超家族 Superfamily superfamilyc.48.1 — TK C-terminal domain-like
家族 Family familyc.48.1.0 — automated matches
结构域编号 domain_idd3dvag_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family familyc.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module
结构域编号 domain_idd3dvah1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family familyc.36.1.0 — automated matches
结构域编号 domain_idd3dvah2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.48 — TK C-terminal domain-like
超家族 Superfamily superfamilyc.48.1 — TK C-terminal domain-like
家族 Family familyc.48.1.0 — automated matches
结构域编号 domain_idd3dvai_
类 Class classa — All alpha proteins
折叠类型 Fold folda.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
超家族 Superfamily superfamilya.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
家族 Family familya.9.1.0 — automated matches
结构域编号 domain_idd3dvaj_
类 Class classa — All alpha proteins
折叠类型 Fold folda.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
超家族 Superfamily superfamilya.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
家族 Family familya.9.1.0 — automated matches

CATH v4.4 (14 domains)

结构域编号 domain_id3dvaA00
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 superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
结构域编号 domain_id3dvaB01
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 superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
结构域编号 domain_id3dvaB02
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 superfamily920 —
结构域编号 domain_id3dvaC00
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 superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
结构域编号 domain_id3dvaD01
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 superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
结构域编号 domain_id3dvaD02
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 superfamily920 —
结构域编号 domain_id3dvaE00
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 superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
结构域编号 domain_id3dvaF01
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 superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
结构域编号 domain_id3dvaF02
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 superfamily920 —
结构域编号 domain_id3dvaG00
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 superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
结构域编号 domain_id3dvaH01
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 superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
结构域编号 domain_id3dvaH02
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 superfamily920 —
结构域编号 domain_id3dvaI00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology320 — Dihydrolipoamide Transferase
同源超家族 H-superfamily homologous superfamily10 — E3-binding domain
结构域编号 domain_id3dvaJ00
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology320 — Dihydrolipoamide Transferase
同源超家族 H-superfamily homologous superfamily10 — E3-binding domain
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7. 引用文献 (1)