6FKZ | pdb_00006fkz

Crystal structure of zebrafish Sirtuin 5 in complex with 3-(phenylthio)succinyl-CPS1 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

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	8063726	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8063726	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	e6fkzA1	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	e6fkzA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_4	ECOD (1.6)
B	SIR2_1st	e6fkzB2	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	e6fkzB1	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
A, B	NAD-dependent protein deacylase sirtuin-5, mitochondrial	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 catalytic activity, acting on a protein acyltransferase activity deacylase activity 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 catalytic activity, acting on a protein acyltransferase activity deacylase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity protein-succinyllysine desuccinylase activity NAD-dependent protein lysine deacylase activity deacetylase activity protein lysine deacetylase activity histone deacetylase activity, NAD-dependent histone deacetylase activity NAD-dependent protein lysine deacetylase activity histone modifying activity protein-glutaryllysine deglutarylase 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 cation binding transition metal ion binding zinc ion binding metal ion binding acyl binding	protein deacylation macromolecule modification protein desuccinylation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process macromolecule deacylation protein modification process peptidyl-lysine modification peptidyl-lysine desuccinylation peptidyl-amino acid modification peptidyl-lysine demalonylation protein deacylation macromolecule modification protein desuccinylation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process macromolecule deacylation protein modification process peptidyl-lysine modification peptidyl-lysine desuccinylation peptidyl-amino acid modification peptidyl-lysine demalonylation protein demalonylation 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	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 nucleus
C [auth E]	3(S)-(phenylthio)succinyl-CPS1 peptide	-	-	-
D [auth H]	3(R)-(phenylthio)succinyl-CPS1 peptide	-	-	-

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	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A, B	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
A, B	IPR003000	Sirtuin family	Family
A, B	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily

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.