4HDA

Crystal structure of human Sirt5 in complex with Fluor-de-Lys peptide and resveratrol

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)
B	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	e4hdaA4	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	e4hdaA3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_4	ECOD (1.6)
B	SIR2_1st	e4hdaB2	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_4	e4hdaB1	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 (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)
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)

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 [auth F]	Fluor-de-Lys peptide	-	-	-
A, B	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 acyltransferase activity deacylase activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups NAD-dependent protein lysine deacylase 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 regulation of 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 cellular process protein metabolic process macromolecule metabolic process protein modification process 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 cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular component organization or biogenesis regulation of metabolic process protein demalonylation protein deglutarylation small molecule biosynthetic process regulation of ketone biosynthetic process ketone metabolic process regulation of 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 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial intermembrane space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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.