1TD2

Crystal Structure of the PdxY Protein from Escherichia coli

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1td2a_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxamine kinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1td2b_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxamine kinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PfkB-like kinase	8027746	4003122	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribokinase-like	8040125	3001268	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8040125	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	PfkB	e1td2A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
B	PfkB	e1td2B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	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 (4.3.0)
B	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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, B	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 identical protein binding protein binding protein homodimerization activity protein dimerization activity	phosphorylation phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process vitamin metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process phosphorylation phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process vitamin metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process small molecule metabolic process water-soluble vitamin metabolic process pyridoxal metabolic process organic hydroxy compound metabolic process aldehyde metabolic process aldehyde biosynthetic process pyridoxal phosphate biosynthetic process cellular metabolic compound salvage pyridoxal 5'-phosphate salvage organophosphate metabolic process organophosphate biosynthetic process organic hydroxy compound biosynthetic process pyridoxal phosphate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004625	Pyridoxine kinase	Family
A, B	IPR023685	Pyridoxal kinase PdxY	Family
A, B	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain
A, B	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.