1UB0 | pdb_00001ub0

Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d1ub0a_	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)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Thiamin biosynthesis kinases	8022509	4000762	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribokinase-like	8034889	3001268	SCOP2 (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		e1ub0A1	A: Rossmann-like	X: Rossmann-related	H: MurCD/PglD N-terminal domain-like	T: Phos_pyr_kin	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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 alcohol metabolic process thiamine metabolic process vitamin metabolic process sulfur compound biosynthetic process thiamine biosynthetic process biosynthetic process alcohol biosynthetic 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 alcohol metabolic process thiamine metabolic process vitamin metabolic process sulfur compound biosynthetic process thiamine biosynthetic process biosynthetic process alcohol biosynthetic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process pyrimidine-containing compound biosynthetic process primary alcohol biosynthetic process thiamine-containing compound 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	IPR004399	Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain	Domain
A	IPR001763	Rhodanese-like domain	Domain
A	IPR029056	Ribokinase-like	Homologous Superfamily
A	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.