6wfn

Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4a) identified using DNA encoded library technology

Method: X-RAY DIFFRACTION D_max: 52.3 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

N-alpha-acetyltransferase 50

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–169	Not recorded	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 crystallization conditions：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	Resolution 1.07 Å R-free 0.201

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6WFN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OB0 Human MAK3 homolog in complex with Acetyl-CoA Deposited 2006-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–169（168 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.80 Å R-free 0.204
2OB0 Human MAK3 homolog in complex with Acetyl-CoA Deposited 2006-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–169（168 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.80 Å R-free 0.204
2OB0 Human MAK3 homolog in complex with Acetyl-CoA Deposited 2006-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–169（168 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 1.80 Å R-free 0.204
2PSW Human MAK3 homolog in complex with CoA Deposited 2007-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–169（168 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.10 Å R-free 0.265
2PSW Human MAK3 homolog in complex with CoA Deposited 2007-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–169（168 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.10 Å R-free 0.265
2PSW Human MAK3 homolog in complex with CoA Deposited 2007-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–169（168 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.10 Å R-free 0.265
3TFY Naa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA Deposited 2011-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.75 Å R-free 0.254
3TFY Naa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA Deposited 2011-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.75 Å R-free 0.254
3TFY Naa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA Deposited 2011-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.75 Å R-free 0.254
4X5K Human NAA50 complex with coenzyme A and an acetylated peptide Deposited 2014-12-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M sodium formate, 20% PEG 3350	Resolution 2.49 Å R-free 0.255
6PPL Cryo-EM structure of human NatE complex (NatA/Naa50) Deposited 2019-07-08	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–169（169 aa）	Not recorded	ACO ACETYL COENZYME A × 2 IHP* INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.02 Å
6PW9 Cryo-EM structure of human NatE/HYPK complex Deposited 2019-07-22	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–169（169 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ACO ACETYL COENZYME *A × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.03 Å
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) Deposited 2020-04-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) Deposited 2020-04-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) Deposited 2020-04-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) Deposited 2020-04-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) Deposited 2020-04-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.29 Å R-free 0.243
6WF3 Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) Deposited 2020-04-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–169（169 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.29 Å R-free 0.243
6WF5 Crystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor (compound 2) Deposited 2020-04-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–169（169 aa）	Not recorded	U44 (2R)-2-hydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.04 Å R-free 0.274
6WF5 Crystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor (compound 2) Deposited 2020-04-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–169（169 aa）	Not recorded	U44 (2R)-2-hydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions 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	Resolution 2.04 Å R-free 0.274
6WFG Crystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 1.87 Å R-free 0.222
6WFO Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4b) identified using DNA encoded library technology Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 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 Deposited 2020-04-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–169（169 aa）	Not recorded	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 crystallization conditions 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	Resolution 1.85 Å R-free 0.240
9F1B Mammalian ternary complex of a translating 80S ribosome, NAC and NatA/E Deposited 2024-04-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 83 PDB declaration: 89-meric	Chain DA 1–169（169 aa）	Not recorded	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 buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.01 Å
9F1C Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E Deposited 2024-04-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 84 PDB declaration: 90-meric	Chain DA 1–169（169 aa）	Not recorded	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 buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.78 Å
9F1D Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPK Deposited 2024-04-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 91-meric	Chain DA 1–169（169 aa）	Not recorded	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 buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.26 Å

14 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NAA50_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–171； UniProt 1–169

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6wfn
Deposition date deposition_date	2020-04-03
Structure title title	Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4a) identified using DNA encoded library technology
Keywords keywords	N-alpha-acetyltransferase 50, Inhibitor complex, DNA encoded library, AcCoA, TRANSFERASE, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.35 Å
Radius of gyration Rg (electron density) rg_electron	14.96 Å
Forward intensity I(0) i0	6790460.00
Molecular weight molecular_weight	18716.0 kDa
Excluded volume excluded_volume	23354 Å³
Envelope volume envelope_volume	25902 Å³
Hydration-shell volume shell_volume	14419 Å³
Envelope diameter envelope_diameter	51.4 Å
Shell Rg shell_rg	21.07 Å
Envelope Rg envelope_rg	15.31 Å
Shape Rg shape_rg	14.97 Å
Total Rg total_rg	16.06 Å
Total atoms total_atoms	1336
Residues n_residues	151
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	52.3 Å
Rg (real space) rg_real	16.21 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	6.7900e+06
I(0) uncertainty (real space) i0_real_error	7.2850e+04
Rg (reciprocal space) rg_reciprocal	16.23 Å
I(0) (reciprocal space) i0_reciprocal	6791000.0000
Solution quality estimate total_estimate	0.8862
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.081
Kurtosis Kurtosis kurtosis	-0.408
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1383000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.995

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	N-alpha-acetyltransferase 50
Molecular weight formula_weight	19571.5 kDa
EC 编号 ec_number	2.3.1.258,2.3.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1533

GSMKGSRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQKRLYIMTLGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYYKRIEPADAHVLQKNLKVPSGQNADVQKTDN

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	ACETYL COENZYME *A
Molecular weight formula_weight	809.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	552.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6wfna_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	6wfnA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

▶

8. Citations (1)

▶

Unit-cell length a length_a	34.430 Å
Unit-cell length b length_b	62.700 Å
Unit-cell length c length_c	38.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.070 Å
Low-resolution limit resolution_low	36.100 Å
R factor r_factor	0.1900
R_work r_work	0.1890
R_free r_free	0.2010

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