3D4W

Crystal structure of Staphylococcal nuclease variant Delta+PHS A109R at cryogenic temperature

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	d3d4wa_	All beta proteins	OB-fold	Staphylococcal nuclease	Staphylococcal nuclease	Staphylococcal nuclease	strain MW2 (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	8069349	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	SNase	e3d4wA1	A: beta barrels	X: OB-fold	H: Staphylococcal nuclease (From Topology)	T: Staphylococcal nuclease	F: SNase	ECOD (1.6)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00565	Staphylococcal nuclease homologue (SNase)	Staphylococcal nuclease homologue	Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 1 ...	Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Thermonuclease	binding organic cyclic compound binding nucleic acid binding endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016071	Staphylococcal nuclease (SNase-like), OB-fold	Domain
A	IPR035437	SNase-like, OB-fold superfamily	Homologous Superfamily
A	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.