6EO0

Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6eo0a1	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	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
A	d6eo0a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
B	d6eo0b1	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	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
B	d6eo0b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
C	d6eo0c1	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	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
C	d6eo0c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
D	d6eo0d1	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	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)
D	d6eo0d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Zebrafish (Danio rerio ) [TaxId: 7955 ],	SCOPe (2.08)

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)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8063726	3001728	SCOP2B (2022-06-29)
D	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	e6eo0A1	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	e6eo0A2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_4	ECOD (1.6)
B	SIR2_1st	e6eo0B2	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	e6eo0B1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_4	ECOD (1.6)
C	SIR2_1st	e6eo0C1	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_4	e6eo0C2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_4	ECOD (1.6)
D	SIR2_1st	e6eo0D1	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_4	e6eo0D2	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)
C	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
C	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)
D	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
D	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, C, D	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, C, D	NAD-dependent protein deacylase sirtuin-5, mitochondrial	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 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase 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 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity protein-succinyllysine desuccinylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds catalytic activity, acting on a protein protein-glutaryllysine deglutarylase activity protein-malonyllysine demalonylase activity cation binding transition metal ion binding zinc ion binding metal ion binding acyl binding transferase activity deacetylase activity protein lysine deacetylase activity acyltransferase activity histone deacetylase activity, NAD-dependent deacylase activity NAD-dependent protein lysine deacylase activity histone deacetylase activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups	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 nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR027546	Sirtuin, class III	Family
A, B, C, D	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B, C, D	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A, B, C, D	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
A, B, C, D	IPR003000	Sirtuin family	Family
A, B, C, D	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.