1RFU | pdb_00001rfu

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)
A	d1rfua_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxal kinase	(Ovis aries ) [TaxId: 9940 ],	SCOPe (2.08)
B	d1rfub_	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)
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)
H	d1rfuh_	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
B	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)
F	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribokinase-like	8043040	3001268	SCOP2B (2022-06-29)
C	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)
A		e1rfuA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
B		e1rfuB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
D		e1rfuD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
E		e1rfuE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
F		e1rfuF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
G		e1rfuG1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
H		e1rfuH1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
C		e1rfuC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)

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)
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)
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)
H	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)

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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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	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 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 pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process phosphorus metabolic 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, 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.