2DDM | pdb_00002ddm

Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene at 2.1 A resolution

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ribokinase-like	8083194	3001268	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribokinase-like	8083194	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	PCNA_N	e2ddmB1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: PCNA_N	ECOD (develop294)
A	PQQ,PQQ_2	e2ddmA1	A: alpha bundles	X: Globin-like	H: Globin-like	T: Globin-like	F: PQQ,PQQ_2	ECOD (develop294)

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	Pyridoxine 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 anion binding adenyl nucleotide 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 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 hydroxymethylpyrimidine kinase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding transition metal ion binding zinc ion binding	thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process pyrimidine-containing compound salvage metabolic compound salvage thiamine biosynthetic process sulfur compound metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process primary alcohol biosynthetic 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 pyrimidine-containing compound salvage metabolic compound salvage thiamine biosynthetic process sulfur compound metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process primary alcohol biosynthetic process pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process alcohol biosynthetic process metabolic process cellular process thiamine salvage thiamine-containing compound biosynthetic process primary alcohol metabolic process vitamin B6 biosynthetic process pyridine-containing compound biosynthetic process aldehyde biosynthetic process aldehyde metabolic process pyridoxal 5'-phosphate salvage organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process vitamin B6 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	IPR004625	Pyridoxine kinase	Family
A, B	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain
A, B	IPR023479	Pyridoxine/pyridoxal/pyridoxamine kinase	Family
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.