6DB2 | pdb_00006db2

X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	Clavaminate synthase-like	8099856	3001848	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		e6db2A1	A: OB-fold	X: Nucleic acid-binding protein	H: Nucleotidyltransferase	T: VP4_haemagglut	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.130.10	Alpha Beta	4-Layer Sandwich	Double-stranded beta-helix	Clavaminate synthase-like	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Alpha-ketoglutarate-dependent L-arginine hydroxylase	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate, L-arginine oxygenase (succinate-forming) activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding	antibiotic metabolic process biosynthetic process metabolic process cellular process antibiotic biosynthetic process	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023966	Arginine beta-hydroxylase, Fe2/alpha-ketoglutarate-dependent	Family
A	IPR003819	TauD/TfdA-like domain	Domain
A	IPR014503	Clavaminate synthase-like	Family
A	IPR053447	Alpha-ketoglutarate-dependent hydroxylase	Family
A	IPR042098	Glutarate 2-hydroxylase 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.