1RFU

Crystal structure of pyridoxal kinase complexed with ADP and PLP

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)
B	d1rfub_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
C	d1rfuc_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
D	d1rfud_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
E	d1rfue_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
H	d1rfuh_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
A	d1rfua_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
F	d1rfuf_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
G	d1rfug_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	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	8043040	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribokinase-like	8043040	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	e1rfuB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
C	PF08543	e1rfuC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
D	PF08543	e1rfuD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
E	PF08543	e1rfuE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
H	PF08543	e1rfuH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
A	PF08543	e1rfuA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
F	PF08543	e1rfuF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF08543	ECOD (1.6)
G	PF08543	e1rfuG1	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)
B	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
C	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
D	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
E	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
H	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
A	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
F	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
G	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, C, D, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	pyridoxal kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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 cation binding metal 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004625	Pyridoxine kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029056	Ribokinase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain

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.