3duf

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

Method: X-RAY DIFFRACTION D_max: 167.7 Å Quality: GOOD

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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

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白异源复合物异源复合物蛋白 × 5 PDB 声明：pentameric（5）与蛋白拷贝数一致	链 A； UniProt 1–369 链 C； UniProt 1–369	未记录	Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MG MAGNESIUM ION × 3 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.263
2	蛋白异源复合物异源复合物蛋白 × 5 PDB 声明：pentameric（5）与蛋白拷贝数一致	链 E； UniProt 1–369 链 G； UniProt 1–369	未记录	Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MG MAGNESIUM ION × 2 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.263

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 3DUF	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 A 1–368（368 aa）链 C 1–368（368 aa）	未记录	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	分辨率 2.00 Å R-free 0.215
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 E 1–368（368 aa）链 G 1–368（368 aa）	未记录	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	分辨率 2.00 Å R-free 0.215
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 A 1–368（368 aa）链 C 1–368（368 aa）	突变：YES 突变：YES	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	分辨率 2.30 Å R-free 0.262
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 E 1–368（368 aa）链 G 1–368（368 aa）	突变：YES 突变：YES	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	分辨率 2.30 Å R-free 0.262
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 A 1–369（369 aa）链 C 1–369（369 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2 PYR PYRUVIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.241
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 E 1–369（369 aa）链 G 1–369（369 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.241
3DVA Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 A 1–369（369 aa）链 C 1–369（369 aa）	突变：I206A 突变：I206A	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.35 Å R-free 0.247
3DVA Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 E 1–369（369 aa）链 G 1–369（369 aa）	突变：I206A 突变：I206A	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.35 Å R-free 0.247

共 4 个其他 PDB 条目、8 个 assembly。打开独立比较页并筛选聚集状态

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	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白异源复合物异源复合物蛋白 × 5 PDB 声明：pentameric（5）与蛋白拷贝数一致	链 B； UniProt 1–325 链 D； UniProt 1–325	未记录	Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MG MAGNESIUM ION × 3 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.263
2	蛋白异源复合物异源复合物蛋白 × 5 PDB 声明：pentameric（5）与蛋白拷贝数一致	链 F； UniProt 1–325 链 H； UniProt 1–325	未记录	Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MG MAGNESIUM ION × 2 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.263

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 3DUF	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 B 1–324（324 aa）链 D 1–324（324 aa）	未记录	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	分辨率 2.00 Å R-free 0.215
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 F 1–324（324 aa）链 H 1–324（324 aa）	未记录	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	分辨率 2.00 Å R-free 0.215
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 B 1–324（324 aa）链 D 1–324（324 aa）	未记录	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	分辨率 2.30 Å R-free 0.262
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 F 1–324（324 aa）链 H 1–324（324 aa）	未记录	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	分辨率 2.30 Å R-free 0.262
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 B 1–325（325 aa）链 D 1–325（325 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2 PYR PYRUVIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.241
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 F 1–325（325 aa）链 H 1–325（325 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.241
3DVA Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 B 1–325（325 aa）链 D 1–325（325 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.35 Å R-free 0.247
3DVA Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 F 1–325（325 aa）链 H 1–325（325 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.35 Å R-free 0.247

共 4 个其他 PDB 条目、8 个 assembly。打开独立比较页并筛选聚集状态

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	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白异源复合物异源复合物蛋白 × 5 PDB 声明：pentameric（5）与蛋白拷贝数一致	链 I； UniProt 1–428	未记录	Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） MG MAGNESIUM ION × 3 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.263
2	蛋白异源复合物异源复合物蛋白 × 5 PDB 声明：pentameric（5）与蛋白拷贝数一致	链 J； UniProt 1–428	未记录	Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） MG MAGNESIUM ION × 2 R1T 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.263

数据库中的同蛋白其他状态

其他 PDB	相对当前条目 3DUF	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1B5S DIHYDROLIPOYL TRANSACETYLASE (E.C.2.3.1.12) CATALYTIC DOMAIN (RESIDUES 184-425) FROM BACILLUS STEAROTHERMOPHILUS 提交 1999-01-10	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 60 PDB 声明：60-meric	链 A 184–425（242 aa）片段：CATALYTIC DOMAIN 链 B 184–425（242 aa）片段：CATALYTIC DOMAIN 链 C 184–425（242 aa）片段：CATALYTIC DOMAIN 链 D 184–425（242 aa）片段：CATALYTIC DOMAIN 链 E 184–425（242 aa）片段：CATALYTIC DOMAIN	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 pH 7；pH 7	分辨率 4.40 Å
1EBD DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED WITH THE BINDING DOMAIN OF THE DIHYDROLIPOAMIDE ACETYLASE 提交 1996-02-03	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 C 129–169（41 aa）片段：BINDING DOMAIN, RESIDUES 130 - 170	未记录	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.60 Å
1LAB THREE-DIMENSIONAL STRUCTURE OF THE LIPOYL DOMAIN FROM BACILLUS STEAROTHERMOPHILUS PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX 提交 1992-09-02	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–80（80 aa）	未记录	未记录非水小分子	SOLUTION NMR mmCIF 未提供已读取条件	分辨率未提供
1LAC THREE-DIMENSIONAL STRUCTURE OF THE LIPOYL DOMAIN FROM BACILLUS STEAROTHERMOPHILUS PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX 提交 1992-09-02	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–80（80 aa）	未记录	未记录非水小分子	SOLUTION NMR mmCIF 未提供已读取条件	分辨率未提供
1W3D NMR structure of the peripheral-subunit binding domain of Bacillus stearothermophilus E2p 提交 2004-07-14	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 118–170（53 aa）片段：RESIDUES 118-170	未记录	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 6.5；298 K；离子强度（mmCIF原始值）20	分辨率未提供
1W4E Peripheral-subunit binding domains from mesophilic, thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions 提交 2004-07-23	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 125–169（45 aa）片段：RESIDUES 125-169	突变：YES	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 5.5；298 K；离子强度（mmCIF原始值）150；压力 1.0 NMR样品组成 95% WATER/5% D2O, 3MM SAMPLE	分辨率未提供
1W4F Peripheral-subunit from mesophilic, thermophilic and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions 提交 2004-07-23	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 125–169（45 aa）片段：RESIDUES 125-169	突变：YES	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 5.5；298 K；离子强度（mmCIF原始值）150；压力 1.0 NMR样品组成 95% H20/5%D20, 3MM SAMPLE	分辨率未提供
1W4G Peripheral-subunit binding domains from mesophilic, thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state folding transitions 提交 2004-07-23	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 125–169（45 aa）片段：RESIDUES 125-169	突变：YES	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 5.5；298 K；离子强度（mmCIF原始值）150；压力 1.0 NMR样品组成 95% WATER/5% D2O, 3MM SAMPLE	分辨率未提供
1W4H Peripheral-subunit from mesophilic, thermophilic and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions 提交 2004-07-23	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 108–152（45 aa）片段：RESIDUES 108-152	未记录	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 7；298 K；离子强度（mmCIF原始值）200；压力 1.0 NMR样品组成 95%WATER/5% D20, 3MM SAMPLE	分辨率未提供
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 I 122–170（49 aa）片段：PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 122-170	未记录	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	分辨率 2.00 Å R-free 0.215
1W85 The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 J 122–170（49 aa）片段：PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 122-170	未记录	MG MAGNESIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 TPP THIAMINE DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00	分辨率 2.00 Å R-free 0.215
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 I 122–170（49 aa）片段：PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 127-169	未记录	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	分辨率 2.30 Å R-free 0.262
1W88 The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2 提交 2004-09-16	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 J 122–170（49 aa）片段：PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 127-169	未记录	MG MAGNESIUM ION × 2 TPP THIAMINE DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 pH 5；15% PEG 4000, 0.2M IMIDAZOLE MALATE PH5, pH 5.00	分辨率 2.30 Å R-free 0.262
2PDD THE HIGH RESOLUTION STRUCTURE OF THE PERIPHERAL SUBUNIT-BINDING DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS STEAROTHERMOPHILUS 提交 1992-11-25	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 128–170（43 aa）	未记录	未记录非水小分子	SOLUTION NMR mmCIF 未提供已读取条件	分辨率未提供
2PDE THE HIGH RESOLUTION STRUCTURE OF THE PERIPHERAL SUBUNIT-BINDING DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX OF BACILLUS STEAROTHERMOPHILUS 提交 1992-11-25	构建体不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 128–170（43 aa）	未记录	未记录非水小分子	SOLUTION NMR mmCIF 未提供已读取条件	分辨率未提供
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 I 1–428（428 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2 PYR PYRUVIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.241
3DV0 Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 J 1–428（428 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP. The crystals were soaked with 10mM pyruvate for 3-day, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.50 Å R-free 0.241
3DVA Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 I 1–428（428 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.35 Å R-free 0.247
3DVA Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex 提交 2008-07-18	配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 5 PDB 声明：pentameric	链 J 1–428（428 aa）	未记录	MG MAGNESIUM ION × 3 TPW 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；The mutant crystals are obtained from sitting-drop vapour diffusion using following condition: 10-15% PEG 4K, 0.2 M imidazole malate pH 5 in the presence of 5 mM 3-deazaThDP, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	分辨率 2.35 Å R-free 0.247
9UKZ dihydrolipoyl acetyl transferase (E2) inner core of the pyruvate dehydrogenase complex 提交 2025-04-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 3 PDB 声明：trimeric	链 A 185–426（242 aa）链 B 185–426（242 aa）链 C 185–426（242 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 4.20 Å

共 16 个其他 PDB 条目、20 个 assembly。打开独立比较页并筛选聚集状态

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。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3duf
沉积日期 deposition_date	2008-07-17
结构标题 title	Snapshots 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 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	48.90 Å
回转半径 Rg (电子) rg_electron	48.79 Å
零角强度 I(0) i0	1362750000.00
分子量 molecular_weight	313130.0 kDa
排除体积 excluded_volume	393940 Å³
包络体积 envelope_volume	500090 Å³
水化壳体积 shell_volume	84029 Å³
包络直径 envelope_diameter	180.4 Å
壳层 Rg shell_rg	53.57 Å
包络 Rg envelope_rg	48.63 Å
形状 Rg shape_rg	48.77 Å
总 Rg total_rg	49.00 Å
总原子数 total_atoms	22073
残基数 n_residues	2830
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	167.7 Å
Rg (实空间) rg_real	49.09 Å
Rg 误差 (实空间) rg_real_error	1.66 Å
I(0) (实空间) i0_real	1.3630e+09
I(0) 误差 (实空间) i0_real_error	2.4640e+07
Rg (倒空间) rg_reciprocal	48.91 Å
I(0) (倒空间) i0_reciprocal	1362000000.0000
解质量估计 total_estimate	0.8635
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	47.1 Å
偏度 Skewness skewness	0.415
峰度 Kurtosis kurtosis	-0.382
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	288500000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.782

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (7)

实体 1 Entity 1 polymer

描述 description	Pyruvate dehydrogenase E1 component subunit alpha
分子量 formula_weight	41518.2 kDa
EC 编号 ec_number	1.2.4.1
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G
原子数 atom_count	22480

MGVKTFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILPGYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQNNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFRKFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK

来源 Source

来源生物 organism	Bacillus stearothermophilus
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 polymer

描述 description	Pyruvate dehydrogenase E1 component subunit beta
分子量 formula_weight	35495.6 kDa
EC 编号 ec_number	1.2.4.1
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H

MAQMTMVQAITDALRIELKNDPNVLIFGEDVGVNGGVFRATEGLQAEFGEDRVFDTPLAESGIGGLAIGLALQGFRPVPEIQFFGFVYEVMDSICGQMARIRYRTGGRYHMPITIRSPFGGGVHTPELHSDSLEGLVAQQPGLKVVIPSTPYDAKGLLISAIRDNDPVIFLEHLKLYRSFRQEVPEGEYTIPIGKADIKREGKDITIIAYGAMVHESLKAAAELEKEGISAEVVDLRTVQPLDIETIIGSVEKTGRAIVVQEAQRQAGIAANVVAEINERAILSLEAPVLRVAAPDTVYPFAQAESVWLPNFKDVIETAKKVMNF

来源 Source

来源生物 organism	Bacillus stearothermophilus
宿主生物 host_organism	Escherichia coli

实体 3 Entity 3 polymer

描述 description	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
分子量 formula_weight	46392.2 kDa
EC 编号 ec_number	2.3.1.12
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	I,J

MAFEFKLPDIGEGIHEGEIVKWFVKPGDEVNEDDVLCEVQNDKAVVEIPSPVKGKVLEILVPEGTVATVGQTLITLDAPGYENMTFKGQEQEEAKKEEKTETVSKEEKVDAVAPNAPAAEAEAGPNRRVIAMPSVRKYAREKGVDIRLVQGTGKNGRVLKEDIDAFLAGGAKPAPAAAEEKAAPAAAKPATTEGEFPETREKMSGIRRAIAKAMVHSKHTAPHVTLMDEADVTKLVAHRKKFKAIAAEKGIKLTFLPYVVKALVSALREYPVLNTSIDDETEEIIQKHYYNIGIAADTDRGLLVPVIKHADRKPIFALAQEINELAEKARDGKLTPGEMKGASCTITNIGSAGGQWFTPVINHPEVAILGIGRIAEKPIVRDGEIVAAPMLALSLSFDHRMIDGATAQKALNHIKRLLSDPELLLMEA

来源 Source

来源生物 organism	Bacillus stearothermophilus
宿主生物 host_organism	Escherichia coli

实体 4 Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

实体 5 Entity 5 non-polymer

描述 description	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE
分子量 formula_weight	467.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 6 Entity 6 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 7 Entity 7 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	407

▼

7. 折叠分类 (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

结构域编号 domain_id	d3dufa_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

结构域编号 domain_id	d3dufb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.0 — automated matches

结构域编号 domain_id	d3dufb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.48 — TK C-terminal domain-like
超家族 Superfamily superfamily	c.48.1 — TK C-terminal domain-like
家族 Family family	c.48.1.0 — automated matches

结构域编号 domain_id	d3dufc_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

结构域编号 domain_id	d3dufd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.0 — automated matches

结构域编号 domain_id	d3dufd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.48 — TK C-terminal domain-like
超家族 Superfamily superfamily	c.48.1 — TK C-terminal domain-like
家族 Family family	c.48.1.0 — automated matches

结构域编号 domain_id	d3dufe_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

结构域编号 domain_id	d3duff1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.0 — automated matches

结构域编号 domain_id	d3duff2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.48 — TK C-terminal domain-like
超家族 Superfamily superfamily	c.48.1 — TK C-terminal domain-like
家族 Family family	c.48.1.0 — automated matches

结构域编号 domain_id	d3dufg_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

结构域编号 domain_id	d3dufh1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
超家族 Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
家族 Family family	c.36.1.0 — automated matches

结构域编号 domain_id	d3dufh2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.48 — TK C-terminal domain-like
超家族 Superfamily superfamily	c.48.1 — TK C-terminal domain-like
家族 Family family	c.48.1.0 — automated matches

结构域编号 domain_id	d3dufi_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
超家族 Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
家族 Family family	a.9.1.0 — automated matches

结构域编号 domain_id	d3dufj_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
超家族 Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
家族 Family family	a.9.1.0 — automated matches

CATH v4.4 (12 domains)

结构域编号 domain_id	3dufA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3dufB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3dufB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	920 —

结构域编号 domain_id	3dufC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3dufD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3dufD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	920 —

结构域编号 domain_id	3dufE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3dufF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3dufF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	920 —

结构域编号 domain_id	3dufG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3dufH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

结构域编号 domain_id	3dufH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	920 —

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	69.247 Å
晶胞边长 b length_b	231.995 Å
晶胞边长 c length_c	92.614 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.74 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	59.440 Å
R 因子 r_factor	0.1923
R_work r_work	0.1885
R_free r_free	0.2630

fit	/app/data/saxs_computation/du/3duf/3duf.fit
pddf	/app/data/pr_computation/du/3duf/3duf.pr.out
profile	/app/data/saxs_computation/du/3duf/3duf.dat

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

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

Pyruvate dehydrogenase E1 component subunit alpha

当前结构中的状态

数据库中的同蛋白其他状态

Pyruvate dehydrogenase E1 component subunit beta

当前结构中的状态

数据库中的同蛋白其他状态

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (7)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 polymer

聚合物 Polymer

来源 Source

实体 3 Entity 3 polymer

聚合物 Polymer

来源 Source

实体 4 Entity 4 non-polymer

实体 5 Entity 5 non-polymer

实体 6 Entity 6 non-polymer

实体 7 Entity 7 water

7. 折叠分类 (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)