6YK0 | pdb_00006yk0

Crystal structure of mouse pyridoxal kinase in complex with ATP-gamma-S

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)
D	d6yk0d_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d6yk0c_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d6yk0b_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d6yk0a_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	automated matches	Mouse (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)
D	SCOP2 Family	PfkB-like kinase	8102912	4003122	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Ribokinase-like	8102913	3001268	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8102913	3001268	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8102913	3001268	SCOP2B (2022-06-29)
A	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)
D	Raptor_N	e6yk0D1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (develop294)
C	Raptor_N	e6yk0C1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (develop294)
B	Raptor_N	e6yk0B1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (develop294)
A	Raptor_N	e6yk0A1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Raptor_N	ECOD (develop294)

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 magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding potassium ion binding alkali metal ion 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 identical protein binding protein binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding sodium ion binding transition metal ion binding zinc ion binding pyridoxal binding	pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process metabolic compound salvage pyridoxal 5'-phosphate salvage pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process metabolic compound salvage pyridoxal 5'-phosphate salvage biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridoxal phosphate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.