6IFC | pdb_00006ifc

Crystal structure of VapBC from Salmonella typhimurium

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G	Cytochrome_C554	e6ifcG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cytochrome_C554	ECOD (v294.1)
E	Cytochrome_C554	e6ifcE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cytochrome_C554	ECOD (v294.1)
C	Cytochrome_C554	e6ifcC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cytochrome_C554	ECOD (v294.1)
A	Dyp_perox_N	e6ifcA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Dyp_perox_N	ECOD (v294.1)
F	PrgH	e6ifcF1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: PrgH	ECOD (v294.1)
B	PrgH	e6ifcB1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: PrgH	ECOD (v294.1)
D	Cytochrome_C554	e6ifcD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Cytochrome_C554	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (utative)
E	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (utative)
C	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (utative)
A	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF01850	PIN domain (PIN)	PIN domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	tRNA(fMet)-specific endonuclease VapC	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity hydrolase activity	-	-
B, F	Antitoxin VapB	DNA binding binding nucleic acid binding	-	-
D, H	Antitoxin VapB	DNA binding binding nucleic acid binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR002716	PIN domain	Domain
A, C, E, G	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR022907	VapC family	Family
A, C, E, G	IPR050556	Type II toxin-antitoxin system RNase	Family
B, F	IPR051734	Type II toxin-antitoxin VapB antitoxins	Family
B, F	IPR047976	Antitoxin VapB2-like	Family
B, F	IPR037914	SpoVT-AbrB domain superfamily	Homologous Superfamily
B, F	IPR007159	SpoVT-AbrB domain	Domain
D, H	IPR051734	Type II toxin-antitoxin VapB antitoxins	Family
D, H	IPR047976	Antitoxin VapB2-like	Family
D, H	IPR037914	SpoVT-AbrB domain superfamily	Homologous Superfamily
D, H	IPR007159	SpoVT-AbrB domain	Domain

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.