1JXI | pdb_00001jxi

4-Amino-5-hydroxymethyl-2-methylpyrimidine Phosphate Kinase from Salmonella typhimurium complexed with 4-Amino-5-hydroxymethyl-2-methylpyrimidine

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	d1jxib_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Thiamin biosynthesis kinases	4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD)	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
A	d1jxia_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Thiamin biosynthesis kinases	4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD)	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	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	8037435	3001268	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribokinase-like	8037435	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	PfkB	e1jxiB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
A	PfkB	e1jxiA1	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)
B	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)

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	PHOSPHOMETHYLPYRIMIDINE 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 phosphomethylpyrimidine kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups hydroxymethylpyrimidine kinase activity phosphotransferase activity, alcohol group as acceptor	pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process thiamine diphosphate metabolic process sulfur compound metabolic process metabolic process pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process thiamine-containing compound metabolic process vitamin biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process thiamine diphosphate metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process thiamine diphosphate biosynthetic process thiamine-containing compound biosynthetic process alcohol metabolic process thiamine metabolic process thiamine biosynthetic process alcohol biosynthetic process primary alcohol biosynthetic process primary alcohol metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004399	Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain	Domain
A, B	IPR029056	Ribokinase-like	Homologous Superfamily
A, B	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.