6wf5

Crystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor (compound 2)

Method: X-RAY DIFFRACTION D_max: 104.4 Å Quality: REASONABLE

▼

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

N-alpha-acetyltransferase 50

Homo sapiens

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 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 1–169	未记录	ACE-MET-LEU-GLY-PRO-NH2 × 1 U44 (2R)-2-hydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；286.15 K；Co-crystallization: Naa50 apo protein (14.3 mg/ml) was incubated with compound 2 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein:ligand complex	分辨率 2.04 Å R-free 0.274
2	蛋白异源复合物异源复合物蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 B； UniProt 1–169	未记录	ACE-MET-LEU-GLY-PRO-NH2 × 1 U44 (2R)-2-hydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, SITTING DROP；286.15 K；Co-crystallization: Naa50 apo protein (14.3 mg/ml) was incubated with compound 2 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein:ligand complex	分辨率 2.04 Å R-free 0.274

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 6WF5	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
2OB0 Human MAK3 homolog in complex with Acetyl-CoA 提交 2006-12-18	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 2–169（168 aa）	非标准单体：是（mmCIF未提供具体位点）	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；298 K；Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of ACOA in 20 mM Hepes pH 7.5, 0.1 M NaCl, 2.5 % 1,2-propandiol, and 10 mM DTT. Cryo: 75% reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50	分辨率 1.80 Å R-free 0.204
2OB0 Human MAK3 homolog in complex with Acetyl-CoA 提交 2006-12-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–169（168 aa）	非标准单体：是（mmCIF未提供具体位点）	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；298 K；Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of ACOA in 20 mM Hepes pH 7.5, 0.1 M NaCl, 2.5 % 1,2-propandiol, and 10 mM DTT. Cryo: 75% reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50	分辨率 1.80 Å R-free 0.204
2OB0 Human MAK3 homolog in complex with Acetyl-CoA 提交 2006-12-18	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 2–169（168 aa）	非标准单体：是（mmCIF未提供具体位点）	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray结晶条件 pH 7.5；298 K；Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of ACOA in 20 mM Hepes pH 7.5, 0.1 M NaCl, 2.5 % 1,2-propandiol, and 10 mM DTT. Cryo: 75% reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50	分辨率 1.80 Å R-free 0.204
2PSW Human MAK3 homolog in complex with CoA 提交 2007-05-07	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 2–169（168 aa）	非标准单体：是（mmCIF未提供具体位点）	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of CoA in 20 mM HEPES pH 7.5, 0.1 M NaCl, 2.5% 1,2-Propanediol, and 10 mM DTT. Cryo: 75% Reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	分辨率 2.10 Å R-free 0.265
2PSW Human MAK3 homolog in complex with CoA 提交 2007-05-07	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 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 2–169（168 aa）	非标准单体：是（mmCIF未提供具体位点）	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of CoA in 20 mM HEPES pH 7.5, 0.1 M NaCl, 2.5% 1,2-Propanediol, and 10 mM DTT. Cryo: 75% Reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	分辨率 2.10 Å R-free 0.265
2PSW Human MAK3 homolog in complex with CoA 提交 2007-05-07	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 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 2–169（168 aa）	非标准单体：是（mmCIF未提供具体位点）	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of CoA in 20 mM HEPES pH 7.5, 0.1 M NaCl, 2.5% 1,2-Propanediol, and 10 mM DTT. Cryo: 75% Reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	分辨率 2.10 Å R-free 0.265
3TFY Naa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA 提交 2011-08-16	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 × 2 PDB 声明：dimeric	链 A 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5；273 K；well solution: 16% PEG 8000, 20% glycerol, 40mM potassium phosphate (monobasic), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	分辨率 2.75 Å R-free 0.254
3TFY Naa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA 提交 2011-08-16	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 × 2 PDB 声明：dimeric	链 B 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5；273 K；well solution: 16% PEG 8000, 20% glycerol, 40mM potassium phosphate (monobasic), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	分辨率 2.75 Å R-free 0.254
3TFY Naa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA 提交 2011-08-16	配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 C 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5；273 K；well solution: 16% PEG 8000, 20% glycerol, 40mM potassium phosphate (monobasic), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	分辨率 2.75 Å R-free 0.254
4X5K Human NAA50 complex with coenzyme A and an acetylated peptide 提交 2014-12-05	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 × 2 PDB 声明：dimeric	链 A 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M sodium formate, 20% PEG 3350	分辨率 2.49 Å R-free 0.255
6PPL Cryo-EM structure of human NatE complex (NatA/Naa50) 提交 2019-07-08	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 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 1–169（169 aa）	未记录	ACO ACETYL COENZYME A × 2 IHP* INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 3.02 Å
6PW9 Cryo-EM structure of human NatE/HYPK complex 提交 2019-07-22	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 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–169（169 aa）	未记录	IHP INOSITOL HEXAKISPHOSPHATE × 1 ACO ACETYL COENZYME *A × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 4.03 Å
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) 提交 2020-04-03	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 × 2 PDB 声明：dimeric	链 A 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；286.15 K；Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex	分辨率 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) 提交 2020-04-03	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 × 2 PDB 声明：dimeric	链 B 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；286.15 K；Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex	分辨率 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) 提交 2020-04-03	配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 C 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；286.15 K；Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex	分辨率 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) 提交 2020-04-03	配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 D 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；286.15 K；Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex	分辨率 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) 提交 2020-04-03	配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 E 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；286.15 K；Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex	分辨率 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) 提交 2020-04-03	配体/离子不同实验环境不同结构质量不同	Assembly 6 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 F 1–169（169 aa）	未记录	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；286.15 K；Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex	分辨率 2.29 Å R-free 0.243
6WFG Crystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology 提交 2020-04-03	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–169（169 aa）	未记录	COA COENZYME A × 1 U3V (2S)-N-[(2S)-3-[1-(3-tert-butyl-1-methyl-1H-pyrazole-5-carbonyl)piperidin-4-yl]-1-(methylamino)-1-oxopropan-2-yl]-6-oxopiperidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；294.15 K；Soak of compound into CoA bound crystals. Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane	分辨率 2.16 Å R-free 0.253
6WFG Crystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology 提交 2020-04-03	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 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 1–169（169 aa）	未记录	COA COENZYME A × 1 U3V (2S)-N-[(2S)-3-[1-(3-tert-butyl-1-methyl-1H-pyrazole-5-carbonyl)piperidin-4-yl]-1-(methylamino)-1-oxopropan-2-yl]-6-oxopiperidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；294.15 K；Soak of compound into CoA bound crystals. Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane	分辨率 2.16 Å R-free 0.253
6WFG Crystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology 提交 2020-04-03	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 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 E 1–169（169 aa）	未记录	COA COENZYME A × 1 U3V (2S)-N-[(2S)-3-[1-(3-tert-butyl-1-methyl-1H-pyrazole-5-carbonyl)piperidin-4-yl]-1-(methylamino)-1-oxopropan-2-yl]-6-oxopiperidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；294.15 K；Soak of compound into CoA bound crystals. Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane	分辨率 2.16 Å R-free 0.253
6WFK Crystal structure of human Naa50 in complex with CoA and an inhibitor (compound 4a) identified using DNA encoded library technology 提交 2020-04-03	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–169（169 aa）	未记录	COA COENZYME A × 1 U2J (4S)-1-methyl-N-{(3S,5S)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；294 K；Compound 4a soaked into crystals of Naa50+CoA. CoA co-crystals: Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane	分辨率 1.87 Å R-free 0.222
6WFK Crystal structure of human Naa50 in complex with CoA and an inhibitor (compound 4a) identified using DNA encoded library technology 提交 2020-04-03	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 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–169（169 aa）	未记录	COA COENZYME A × 1 U2J (4S)-1-methyl-N-{(3S,5S)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；294 K；Compound 4a soaked into crystals of Naa50+CoA. CoA co-crystals: Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane	分辨率 1.87 Å R-free 0.222
6WFK Crystal structure of human Naa50 in complex with CoA and an inhibitor (compound 4a) identified using DNA encoded library technology 提交 2020-04-03	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 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 1–169（169 aa）	未记录	COA COENZYME A × 1 U2J (4S)-1-methyl-N-{(3S,5S)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；294 K；Compound 4a soaked into crystals of Naa50+CoA. CoA co-crystals: Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane	分辨率 1.87 Å R-free 0.222
6WFN Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4a) identified using DNA encoded library technology 提交 2020-04-03	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–169（169 aa）	未记录	ACO ACETYL COENZYME A × 1 U2J* (4S)-1-methyl-N-{(3S,5S)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.77；294 K；Naa50 apo protein (13.0 mg/ml) was incubated with 4a and AcCoA in a 1:3:3 molar ratio on ice for 60 min. Reservoir solution containing 0.1 M Bis_tris, pH 5.77 and 21% w/v PEG 3350 was mixed 0.2ul:0.2ul with Naa50:4b:AcCoA complex	分辨率 1.07 Å R-free 0.201
6WFO Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4b) identified using DNA encoded library technology 提交 2020-04-03	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 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 1–169（169 aa）	未记录	ACO ACETYL COENZYME A × 1 U3Y* (4S)-1-methyl-N-{(3S,5R)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.77；294 K；Naa50 apo protein (13.0 mg/ml) was incubated with 4b and AcCoA in a 1:3:3 molar ratio on ice for 60 min. Reservoir solution of 0.1 M Bis_tris, pH 5.77 and 24% w/v PEG 3350 was mixed 0.2ul:0.2ul with Naa50:4b:AcCoA complex	分辨率 1.85 Å R-free 0.240
6WFO Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4b) identified using DNA encoded library technology 提交 2020-04-03	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 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 1–169（169 aa）	未记录	ACO ACETYL COENZYME A × 1 U3Y* (4S)-1-methyl-N-{(3S,5R)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.77；294 K；Naa50 apo protein (13.0 mg/ml) was incubated with 4b and AcCoA in a 1:3:3 molar ratio on ice for 60 min. Reservoir solution of 0.1 M Bis_tris, pH 5.77 and 24% w/v PEG 3350 was mixed 0.2ul:0.2ul with Naa50:4b:AcCoA complex	分辨率 1.85 Å R-free 0.240
6WFO Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4b) identified using DNA encoded library technology 提交 2020-04-03	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 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 1–169（169 aa）	未记录	ACO ACETYL COENZYME A × 1 U3Y* (4S)-1-methyl-N-{(3S,5R)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.77；294 K；Naa50 apo protein (13.0 mg/ml) was incubated with 4b and AcCoA in a 1:3:3 molar ratio on ice for 60 min. Reservoir solution of 0.1 M Bis_tris, pH 5.77 and 24% w/v PEG 3350 was mixed 0.2ul:0.2ul with Naa50:4b:AcCoA complex	分辨率 1.85 Å R-free 0.240
9F1B Mammalian ternary complex of a translating 80S ribosome, NAC and NatA/E 提交 2024-04-18	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 信息不足异源复合物；蛋白 × 83 PDB 声明：89-meric	链 DA 1–169（169 aa）	未记录	MG MAGNESIUM ION × 420 ZN ZINC ION × 8 UNX UNKNOWN LIGAND × 306 IHP INOSITOL HEXAKISPHOSPHATE × 1 SPD SPERMIDINE × 30 SPM SPERMINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.4 cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE	分辨率 3.01 Å
9F1C Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E 提交 2024-04-18	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 信息不足异源复合物；蛋白 × 84 PDB 声明：90-meric	链 DA 1–169（169 aa）	未记录	UNX UNKNOWN LIGAND × 277 MG MAGNESIUM ION × 420 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SPD SPERMIDINE × 30 SPM SPERMINE × 3 ZN ZINC ION × 8 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.4 cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE	分辨率 3.78 Å
9F1D Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK 提交 2024-04-18	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–RNA 异源复合物；蛋白 × 85 PDB 声明：91-meric	链 DA 1–169（169 aa）	未记录	UNX UNKNOWN LIGAND × 295 SPD SPERMIDINE × 30 MG MAGNESIUM ION × 420 SPM SPERMINE × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.4 cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE	分辨率 3.26 Å

共 14 个其他 PDB 条目、31 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	NAA50_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 3–171； UniProt 1–169 作者链 B； PDB构建体 3–171； UniProt 1–169

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

▼

2. 结构基本信息 2. Structure Basics

条目编号 entry_id	6wf5
沉积日期 deposition_date	2020-04-03
结构标题 title	Crystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor (compound 2)
关键词 keywords	N-alpha-acetyltransferase 50, Inhibitor complex, TRANSFERASE, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	26.85 Å
回转半径 Rg (电子) rg_electron	25.98 Å
零角强度 I(0) i0	24388600.00
分子量 molecular_weight	38644.0 kDa
排除体积 excluded_volume	48827 Å³
包络体积 envelope_volume	63470 Å³
水化壳体积 shell_volume	21905 Å³
包络直径 envelope_diameter	111.3 Å
壳层 Rg shell_rg	30.81 Å
包络 Rg envelope_rg	27.05 Å
形状 Rg shape_rg	26.01 Å
总 Rg total_rg	26.49 Å
总原子数 total_atoms	2717
残基数 n_residues	332
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

▼

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

最大尺寸 Dmax dmax	104.4 Å
Rg (实空间) rg_real	27.20 Å
Rg 误差 (实空间) rg_real_error	1.18 Å
I(0) (实空间) i0_real	2.4390e+07
I(0) 误差 (实空间) i0_real_error	3.9930e+05
Rg (倒空间) rg_reciprocal	27.09 Å
I(0) (倒空间) i0_reciprocal	24390000.0000
解质量估计 total_estimate	0.7178
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	23.0 Å
偏度 Skewness skewness	0.625
峰度 Kurtosis kurtosis	-0.098
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9761000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.380; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.199; Smooth: 0.986

▶

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

▶

6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	N-alpha-acetyltransferase 50
分子量 formula_weight	19571.5 kDa
EC 编号 ec_number	2.3.1.258,2.3.1.-
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	A,B
原子数 atom_count	2815

GSMKGSRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQKRLYIMTLGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYYKRIEPADAHVLQKNLKVPSGQNADVQKTDN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

实体 2 Entity 2 polymer

描述 description	ACE-MET-LEU-GLY-PRO-NH2
分子量 formula_weight	440.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	C,D

XMLGPX

实体 3 Entity 3 non-polymer

描述 description	(2R)-2-hydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide
分子量 formula_weight	262.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 4 Entity 4 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	98

▼

7. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	6wf5A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

结构域编号 domain_id	6wf5B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

▶

8. 引用文献 (1)

▶

晶胞边长 a length_a	50.937 Å
晶胞边长 b length_b	52.339 Å
晶胞边长 c length_c	64.123 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	97.38 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.040 Å
最低分辨率 resolution_low	50.520 Å
R 因子 r_factor	0.2240
R_work r_work	0.2220
R_free r_free	0.2740

fit	/app/data/saxs_computation/wf/6wf5/6wf5.fit
pddf	/app/data/pr_computation/wf/6wf5/6wf5.pr.out
profile	/app/data/saxs_computation/wf/6wf5/6wf5.dat

Crystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor (compound 2)

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

N-alpha-acetyltransferase 50

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 (4)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 non-polymer

实体 4 Entity 4 water

7. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)