3RIG | pdb_00003rig

Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3rigb1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Sir2 family of transcriptional regulators	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rigb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3riga1	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Sir2 family of transcriptional regulators	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3riga2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8037646	3001728	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8037646	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)
B		e3rigB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: PK_Tyr_Ser-Thr	F:	ECOD (20:10:01)
A		e3rigA1	A: Alpha-beta plaits	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: OTCace	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
B	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)
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, B	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	peptide of histone 3 thioacetyl-lysine 9	DNA binding binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity 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 regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	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 protein-DNA complex 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 protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B	NAD-dependent deacetylase sirtuin-5	catalytic activity, acting on a protein acyltransferase activity deacylase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity protein-glutaryllysine deglutarylase activity catalytic activity NAD-dependent protein lysine deacylase activity protein-malonyllysine demalonylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds NAD+ binding NAD binding catalytic activity, acting on a protein acyltransferase activity deacylase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity protein-glutaryllysine deglutarylase activity catalytic activity NAD-dependent protein lysine deacylase activity protein-malonyllysine demalonylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding protein-succinyllysine desuccinylase activity deacetylase activity protein lysine deacetylase activity histone deacetylase activity, NAD-dependent histone deacetylase activity NAD-dependent protein lysine deacetylase activity histone modifying activity cation binding transition metal ion binding zinc ion binding metal ion binding	peptidyl-lysine modification protein desuccinylation primary metabolic process macromolecule deacylation protein deacylation peptidyl-lysine desuccinylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process response to stimulus peptidyl-lysine modification protein desuccinylation primary metabolic process macromolecule deacylation protein deacylation peptidyl-lysine desuccinylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process response to stimulus response to stress response to ischemia protein demalonylation protein deglutarylation regulation of biosynthetic process regulation of biological process regulation of cellular process small molecule biosynthetic process regulation of ketone biosynthetic process ketone metabolic process biological regulation regulation of ketone metabolic process biosynthetic process regulation of small molecule metabolic process small molecule metabolic process regulation of metabolic process ketone biosynthetic process negative regulation of metabolic process reactive oxygen species metabolic process negative regulation of biological process negative regulation of reactive oxygen species metabolic process negative regulation of cellular process regulation of reactive oxygen species metabolic process peptidyl-lysine demalonylation protein deacetylation negative regulation of cardiac muscle cell apoptotic process muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cell death cardiac muscle cell apoptotic process negative regulation of apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process negative regulation of muscle cell apoptotic process negative regulation of striated muscle cell apoptotic process apoptotic process programmed cell death response to nutrient levels cellular component organization organelle organization cellular component organization or biogenesis mitochondrion organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial intermembrane space organelle envelope lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR009072	Histone-fold	Homologous Superfamily
C, D	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, D	IPR000164	Histone H3/CENP-A	Family
A, B	IPR027546	Sirtuin, class III	Family
A, B	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B	IPR003000	Sirtuin family	Family
A, B	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A, B	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
A, B	Pharos: Q9NXA8	astrocytic tumor large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor lung cancer osteosarcoma schizophrenia glioblastoma malignant glioma pilocytic astrocytoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.