6S0T | pdb_00006s0t

The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, sulfate, soaked with iodide

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)
B	PhyH_1	e6s0tB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
D	PhyH_1	e6s0tD1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
E	PhyH_1	e6s0tE1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
F	PhyH_1	e6s0tF1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
A	PhyH_1	e6s0tA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)
C	PhyH_1	e6s0tC1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: PhyH_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
D	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
E	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
F	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
A	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)
C	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF05721	Phytanoyl-CoA dioxygenase (PhyH) (PhyH)	Phytanoyl-CoA dioxygenase (PhyH)	This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficie ...	This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Kanamycin B dioxygenase	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity	aminoglycoside antibiotic biosynthetic process carbohydrate derivative biosynthetic process kanamycin metabolic process polyol metabolic process glycosyl compound metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process glycoside metabolic process carbohydrate derivative metabolic process kanamycin biosynthetic process alcohol metabolic process antibiotic biosynthetic process glycoside biosynthetic process antibiotic metabolic process aminoglycoside antibiotic metabolic process aminoglycoside antibiotic biosynthetic process carbohydrate derivative biosynthetic process kanamycin metabolic process polyol metabolic process glycosyl compound metabolic process glycosyl compound biosynthetic process small molecule biosynthetic process glycoside metabolic process carbohydrate derivative metabolic process kanamycin biosynthetic process alcohol metabolic process antibiotic biosynthetic process glycoside biosynthetic process antibiotic metabolic process aminoglycoside antibiotic metabolic process biosynthetic process polyol biosynthetic process alcohol biosynthetic process metabolic process cellular process small molecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR051961	Fungal Secondary Metabolite Dioxygenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR008775	Phytanoyl-CoA dioxygenase-like	Family

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.