4YIJ | pdb_00004yij

Crystal structure of Staphylcoccal nuclease variant Delta+PHS A109E at cryogenic temperature

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4yija_	All beta proteins	OB-fold	Staphylococcal nuclease	Staphylococcal nuclease	Staphylococcal nuclease	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d4yijb_	All beta proteins	OB-fold	Staphylococcal nuclease	Staphylococcal nuclease	Staphylococcal nuclease	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Staphylococcal nuclease	8041753	3000443	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Staphylococcal nuclease	8041753	3000443	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	Cupin_1	e4yijA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: Cupin_1	ECOD (v294.1)
B	VipB_2	e4yijB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: VipB_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.90	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.90	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Nuclease A	binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity 3' overhang single-stranded DNA endonuclease activity DNA endonuclease activity single-stranded DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity cation binding binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity 3' overhang single-stranded DNA endonuclease activity DNA endonuclease activity single-stranded DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity cation binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure membrane extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016071	Staphylococcal nuclease (SNase-like), OB-fold	Domain
A, B	IPR035437	SNase-like, OB-fold superfamily	Homologous Superfamily
A, B	IPR002071	Thermonuclease active site	Active Site

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.