5ZGC | pdb_00005zgc

Crystal Structure of SIRT3 in complex with H4K16bhb peptide

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)
E	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
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)
F	SIR2_1st	e5zgcF2	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)
F	SIR2_2nd_1	e5zgcF1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
E	SIR2_1st	e5zgcE1	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)
E	SIR2_2nd_1	e5zgcE2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
D	SIR2_1st	e5zgcD1	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)
D	SIR2_2nd_1	e5zgcD2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
C	SIR2_1st	e5zgcC1	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)
C	SIR2_2nd_1	e5zgcC2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
B	SIR2_1st	e5zgcB2	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)
B	SIR2_2nd_1	e5zgcB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
A	SIR2_1st	e5zgcA1	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	e5zgcA2	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)
F	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
E	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
E	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
D	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
D	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
C	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
C	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
B	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
B	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)
A	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (utative)
A	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	Histone H4K16bhb peptide	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization telomere organization chromosome organization localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to CENP-A containing chromatin intracellular protein localization multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process regulation of megakaryocyte differentiation negative regulation of biological process cell development megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome membraneless organelle chromosome, centromeric region chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B, C, D, E A, B, C, D, E, F	NAD-dependent protein deacetylase sirtuin-3, mitochondrial	NAD-dependent protein lysine delactylase activity catalytic activity, acting on a protein acyltransferase activity deacylase activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity NAD-dependent protein lysine deacylase activity deacetylase activity protein lysine deacetylase activity sequence-specific DNA binding DNA binding binding NAD-dependent protein lysine delactylase activity catalytic activity, acting on a protein acyltransferase activity deacylase activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity NAD-dependent protein lysine deacylase activity deacetylase activity protein lysine deacetylase activity sequence-specific DNA binding DNA binding binding nucleic acid binding 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 histone deacetylase activity, NAD-dependent histone deacetylase activity histone modifying activity cation binding transition metal ion binding zinc ion binding metal ion binding protein binding enzyme binding	regulation of molecular function positive regulation of molecular function positive regulation of catalase activity regulation of catalytic activity biological regulation positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity peptidyl-lysine deacetylation peptidyl-lysine modification primary metabolic process macromolecule deacylation protein deacetylation protein deacylation regulation of molecular function positive regulation of molecular function positive regulation of catalase activity regulation of catalytic activity biological regulation positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity peptidyl-lysine deacetylation peptidyl-lysine modification primary metabolic process macromolecule deacylation protein deacetylation protein deacylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process aerobic respiration cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy cellular response to stimulus regulation of cellular process 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 biological process 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 cellular response to stress response to stress negative regulation of metabolic process reactive oxygen species 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 positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization localization positive regulation of insulin secretion intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels 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 regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport positive regulation of biological process positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of cellular process positive regulation of peptide secretion regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion positive regulation of signaling oxidative phosphorylation positive regulation of oxidative phosphorylation regulation of generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration positive regulation of cellular respiration positive regulation of metabolic process regulation of oxidative phosphorylation regulation of amide metabolic process sphingolipid biosynthetic process regulation of lipid metabolic process positive regulation of ceramide biosynthetic process lipid biosynthetic process positive regulation of sphingolipid biosynthetic process regulation of primary metabolic process cellular component biogenesis regulation of sphingolipid biosynthetic process positive regulation of biosynthetic process positive regulation of lipid metabolic process amide metabolic process cellular component organization or biogenesis regulation of ceramide biosynthetic process regulation of biosynthetic process membrane lipid metabolic process ceramide metabolic process regulation of membrane lipid metabolic process sphingolipid metabolic process amide biosynthetic process regulation of macromolecule metabolic process regulation of cellular component biogenesis macromolecule biosynthetic process biosynthetic process positive regulation of lipid biosynthetic process ceramide biosynthetic process positive regulation of amide metabolic process regulation of macromolecule biosynthetic process regulation of lipid biosynthetic process membrane lipid biosynthetic process lipid metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I, J, K G, H, I, J, K, L	IPR009072	Histone-fold	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR035425	CENP-T/Histone H4, histone fold	Domain
G, H, I, J, K G, H, I, J, K, L	IPR001951	Histone H4	Family
G, H, I, J, K G, H, I, J, K, L	IPR019809	Histone H4, conserved site	Conserved Site
G, H, I, J, K G, H, I, J, K, L	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003000	Sirtuin family	Family
A, B, C, D, E A, B, C, D, E, F	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A, B, C, D, E A, B, C, D, E, F	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G, H, I, J, K G, H, I, J, K, L	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma ulcerative colitis allergic rhinitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma
A, B, C, D, E A, B, C, D, E, F	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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.