6ACO

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120

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	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)
A	SIR2_1st	e6acoA1	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_4	e6acoA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_4	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 (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	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 deacylase sirtuin-5, mitochondrial	catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity protein-glutaryllysine deglutarylase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds protein-malonyllysine demalonylase activity transferase activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity protein-glutaryllysine deglutarylase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds protein-malonyllysine demalonylase activity transferase activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding protein-succinyllysine desuccinylase activity deacetylase activity protein lysine deacetylase activity NAD-dependent protein lysine deacetylase 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 protein metabolic process macromolecule metabolic process protein modification process regulation of cellular process cellular biosynthetic process peptidyl-lysine modification protein desuccinylation primary metabolic process macromolecule deacylation protein deacylation peptidyl-lysine desuccinylation macromolecule modification peptidyl-amino acid modification metabolic process protein metabolic process macromolecule metabolic process protein modification process regulation of cellular process cellular biosynthetic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process cellular process regulation of macromolecule biosynthetic process regulation of metabolic process protein demalonylation protein deglutarylation regulation of cellular ketone metabolic process small molecule biosynthetic process regulation of ketone biosynthetic process cellular ketone metabolic process regulation of small molecule metabolic process small molecule metabolic process ketone biosynthetic process negative regulation of metabolic process reactive oxygen species metabolic process negative regulation of biological process negative regulation of cellular metabolic 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 response to stimulus organelle organization mitochondrion organization	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial intermembrane space membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial intermembrane space organelle envelope lumen organelle envelope mitochondrial envelope nucleus
B	succinyl peptide H2BK120	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin identical protein binding	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 biological process involved in interspecies interaction between organisms 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 biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus mucosal immune response organ or tissue specific immune response humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide antibacterial humoral response defense response to bacterium response to bacterium defense response to Gram-positive bacterium	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol protein-containing complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol protein-containing complex protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027546	Sirtuin, class III	Family
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	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR007125	Histone H2A/H2B/H3	Domain
B	IPR000558	Histone H2B	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NXA8	astrocytic tumor large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor lung cancer osteosarcoma schizophrenia glioblastoma malignant glioma pilocytic astrocytoma
B	Pharos: P62807	breast carcinoma lung adenocarcinoma breast cancer lung carcinoma Malignant neoplasm of breast ovarian cancer ulcerative colitis autism spectrum disorder exocrine pancreatic carcinoma hypertensive disorder malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma psoriasis allergic rhinitis breast carcinoma lung adenocarcinoma breast cancer lung carcinoma Malignant neoplasm of breast ovarian cancer ulcerative colitis autism spectrum disorder exocrine pancreatic carcinoma hypertensive disorder malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma psoriasis allergic rhinitis cutaneous lupus erythematosus ductal breast carcinoma in situ glioblastoma interstitial cystitis lung cancer malignant mesothelioma osteoarthritis squamous cell lung carcinoma atypical teratoid rhabdoid tumor cystic fibrosis endogenous depression gout invasive ductal breast carcinoma

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.