6YJZ

Crystal structure of mouse pyridoxal kinase in apo form

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	d6yjzb_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d6yjzd_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d6yjza_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d6yjzc_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ribokinase-like	8102913	3001268	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribokinase-like	8102913	3001268	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribokinase-like	8102913	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8102913	3001268	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)
B	PF08543	e6yjzB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
D	PF08543	e6yjzD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
A	PF08543	e6yjzA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
C	PF08543	e6yjzC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08543	Phosphomethylpyrimidine kinase (Phos_pyr_kin)	Phosphomethylpyrimidine kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Pyridoxal Kinase	cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding kinase activity transferase activity catalytic activity pyridoxal kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups lithium ion binding cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding kinase activity transferase activity catalytic activity pyridoxal kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups lithium ion binding vitamin binding vitamin B6 binding pyridoxal phosphate binding organic cyclic compound binding anion binding heterocyclic compound binding magnesium ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding carbohydrate derivative binding ribonucleotide binding identical protein binding protein binding protein homodimerization activity protein dimerization activity sodium ion binding transition metal ion binding zinc ion binding pyridoxal binding	organonitrogen compound metabolic process organic hydroxy compound metabolic process vitamin metabolic process organic cyclic compound metabolic process organic substance metabolic process pyridine-containing compound metabolic process pyridoxamine metabolic process vitamin B6 metabolic process small molecule metabolic process metabolic process water-soluble vitamin metabolic process regulation of biological process regulation of cellular process negative regulation of programmed cell death organonitrogen compound metabolic process organic hydroxy compound metabolic process vitamin metabolic process organic cyclic compound metabolic process organic substance metabolic process pyridine-containing compound metabolic process pyridoxamine metabolic process vitamin B6 metabolic process small molecule metabolic process metabolic process water-soluble vitamin metabolic process regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death cellular metabolic process pyridoxal metabolic process cellular aldehyde metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process phosphorus metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic hydroxy compound biosynthetic process organic cyclic compound biosynthetic process pyridoxal phosphate metabolic process pyridoxine metabolic process phosphorylation cellular metabolic compound salvage pyridoxal 5'-phosphate salvage	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004625	Pyridoxine kinase	Family
A, B, C, D	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain
A, B, C, D	IPR029056	Ribokinase-like	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 R01GM133198.