5ZWB

Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via a Schiff base

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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	SCOP2 Family	PfkB-like kinase	8096183	4003122	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribokinase-like	8096184	3001268	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8096184	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)
A	PF08543	e5zwbA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
B	PF08543	e5zwbB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (utative)
B	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08543	Phosphomethylpyrimidine kinase (Phos_pyr_kin)	Phosphomethylpyrimidine kinase	-	Family
B	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	Pyridoxine/pyridoxal/pyridoxamine 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 organic cyclic compound binding anion 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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding kinase activity transferase activity catalytic activity pyridoxal kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transition metal ion binding zinc ion binding	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process cellular biosynthetic process organic hydroxy compound metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process organic substance metabolic process pyridoxal phosphate biosynthetic process cellular aldehyde metabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process cellular biosynthetic process organic hydroxy compound metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process organic substance metabolic process pyridoxal phosphate biosynthetic process cellular aldehyde metabolic process organic substance biosynthetic process pyridine-containing compound metabolic process small molecule metabolic process water-soluble vitamin metabolic process cellular metabolic compound salvage vitamin B6 biosynthetic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin metabolic process organic cyclic compound metabolic process pyridoxal 5'-phosphate salvage biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic hydroxy compound biosynthetic process organic cyclic compound biosynthetic process vitamin B6 metabolic process pyridoxal phosphate metabolic process	-
B	Pyridoxine/pyridoxal/pyridoxamine 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 organic cyclic compound binding anion 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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding kinase activity transferase activity catalytic activity pyridoxal kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transition metal ion binding zinc ion binding	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process cellular biosynthetic process organic hydroxy compound metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process organic substance metabolic process pyridoxal phosphate biosynthetic process cellular aldehyde metabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process cellular biosynthetic process organic hydroxy compound metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process organic substance metabolic process pyridoxal phosphate biosynthetic process cellular aldehyde metabolic process organic substance biosynthetic process pyridine-containing compound metabolic process small molecule metabolic process water-soluble vitamin metabolic process cellular metabolic compound salvage vitamin B6 biosynthetic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin metabolic process organic cyclic compound metabolic process pyridoxal 5'-phosphate salvage biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic hydroxy compound biosynthetic process organic cyclic compound biosynthetic process vitamin B6 metabolic process pyridoxal phosphate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004625	Pyridoxine kinase	Family
A	IPR029056	Ribokinase-like	Homologous Superfamily
A	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain
A	IPR023479	Pyridoxine/pyridoxal/pyridoxamine kinase	Family
B	IPR004625	Pyridoxine kinase	Family
B	IPR029056	Ribokinase-like	Homologous Superfamily
B	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain
B	IPR023479	Pyridoxine/pyridoxal/pyridoxamine kinase	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.