4BVG

CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SIR2_1st	e4bvgA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
A	SIR2_2nd_1	e4bvgA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
A	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL	deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein NAD-dependent protein deacetylase activity hydrolase activity catalytic activity sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding transferase activity NAD+ binding NAD binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein NAD-dependent protein deacetylase activity hydrolase activity catalytic activity sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding transferase activity NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding cation binding transition metal ion binding zinc ion binding metal ion binding protein binding enzyme binding NAD-dependent histone deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity histone modifying activity	positive regulation of peroxidase activity regulation of biological process regulation of cellular process regulation of catalytic activity biological regulation positive regulation of biological process regulation of peroxidase activity positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity regulation of molecular function positive regulation of molecular function positive regulation of catalase activity regulation of catalase activity positive regulation of peroxidase activity regulation of biological process regulation of cellular process regulation of catalytic activity biological regulation positive regulation of biological process regulation of peroxidase activity positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity regulation of molecular function positive regulation of molecular function positive regulation of catalase activity regulation of catalase activity cellular process positive regulation of cellular process peptidyl-lysine deacetylation organonitrogen compound metabolic process peptidyl-lysine modification primary metabolic process macromolecule deacylation protein deacetylation protein deacylation organic substance metabolic process macromolecule modification peptidyl-amino acid modification nitrogen compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process aerobic respiration cellular respiration energy derivation by oxidation of organic compounds cellular metabolic process generation of precursor metabolites and energy cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade negative regulation of metabolic process reactive oxygen species metabolic process regulation of cellular metabolic process negative regulation of cellular metabolic process negative regulation of reactive oxygen species metabolic process regulation of metabolic process regulation of reactive oxygen species metabolic process regulation of superoxide dismutase activity positive regulation of superoxide dismutase activity protein localization positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization localization cellular macromolecule localization positive regulation of insulin secretion regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels organic substance transport positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion positive regulation of protein localization cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion secretion by cell regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion positive regulation of signaling regulation of amide metabolic process sphingolipid biosynthetic process regulation of lipid metabolic process organonitrogen compound biosynthetic process positive regulation of ceramide biosynthetic process cellular nitrogen compound biosynthetic process regulation of primary metabolic process regulation of nitrogen compound metabolic process cellular component biogenesis positive regulation of metabolic process organic substance biosynthetic process positive regulation of lipid metabolic process membrane lipid metabolic process regulation of membrane lipid metabolic process amide biosynthetic process cellular nitrogen compound metabolic process biosynthetic process ceramide biosynthetic process cellular lipid metabolic process regulation of macromolecule biosynthetic process cellular biosynthetic process lipid biosynthetic process positive regulation of cellular metabolic process positive regulation of sphingolipid biosynthetic process regulation of sphingolipid biosynthetic process positive regulation of biosynthetic process amide metabolic process cellular component organization or biogenesis regulation of ceramide biosynthetic process ceramide metabolic process regulation of biosynthetic process sphingolipid metabolic process regulation of macromolecule metabolic process regulation of cellular component biogenesis macromolecule biosynthetic process regulation of cellular biosynthetic process positive regulation of nitrogen compound metabolic process positive regulation of lipid biosynthetic process positive regulation of amide metabolic process membrane lipid biosynthetic process regulation of lipid biosynthetic process positive regulation of cellular biosynthetic process lipid metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex mitochondrial matrix
B	ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding CoA-ligase activity propionate-CoA ligase activity fatty acid ligase activity ligase activity, forming carbon-sulfur bonds short-chain fatty acid-CoA ligase activity catalytic activity acid-thiol ligase activity ligase activity ATP-dependent activity acetate-CoA ligase activity cation binding AMP binding	monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process acetate metabolic process acetate biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular metabolic process carboxylic acid metabolic process acetate metabolic process acetate biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process short-chain fatty acid metabolic process lipid biosynthetic process propionate metabolic process fatty acid metabolic process primary metabolic process fatty acid biosynthetic process short-chain fatty acid biosynthetic process cellular lipid metabolic process propionate biosynthetic process lipid metabolic process nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process acetyl-CoA metabolic process cellular nitrogen compound biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process heterocycle metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process thioester metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process cellular nitrogen compound metabolic process amide biosynthetic process nucleotide metabolic process organic cyclic compound metabolic process sulfur compound biosynthetic process aromatic compound biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate metabolic process thioester biosynthetic process purine nucleotide metabolic process acyl-CoA metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process nitrogen compound metabolic process purine nucleoside bisphosphate biosynthetic process amide metabolic process carbohydrate derivative biosynthetic process organonitrogen compound metabolic process nucleoside bisphosphate biosynthetic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process organophosphate metabolic process cellular aromatic compound metabolic process acetyl-CoA biosynthetic process from acetate	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR026590	Sirtuin family, catalytic core domain	Domain
A	IPR003000	Sirtuin family	Family
A	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
B	IPR011904	Acetate-CoA ligase	Family
B	IPR020845	AMP-binding, conserved site	Conserved Site
B	IPR045851	AMP-binding enzyme, C-terminal domain superfamily	Homologous Superfamily
B	IPR042099	ANL, N-terminal domain	Homologous Superfamily
B	IPR025110	AMP-binding enzyme, C-terminal domain	Domain
B	IPR000873	AMP-dependent synthetase/ligase domain	Domain
B	IPR032387	Acetyl-coenzyme A synthetase, N-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NTG7	obesity disorder squamous cell carcinoma gestational diabetes benign prostatic hyperplasia DOID:0081062 heart disease neurodegenerative disease osteosarcoma type 2 diabetes mellitus brain aneurysm psoriasis uterine corpus leiomyoma breast cancer Hashimoto thyroiditis oral cavity neoplasm
B	Pharos: Q9NUB1	adrenal cortex carcinoma large cell medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor malignant ependymoma facioscapulohumeral muscular dystrophy medulloblastoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.