1VI9 | pdb_00001vi9

Crystal structure of pyridoxamine kinase

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1vi9d1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxamine kinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1vi9d3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1vi9d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1vi9c1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxamine kinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1vi9c3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1vi9c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1vi9b1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxamine kinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1vi9b3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1vi9b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1vi9a1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	PfkB-like kinase	Pyridoxamine kinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1vi9a3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1vi9a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ribokinase-like	8040125	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8040125	3001268	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8040125	3001268	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribokinase-like	8040125	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)
D	PfkB	e1vi9D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
C	PfkB	e1vi9C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
B	PfkB	e1vi9B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
A	PfkB	e1vi9A1	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)
D	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)
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, C, D	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	Pyridoxamine 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	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process vitamin metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process pyridoxal metabolic process aldehyde metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process vitamin metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process pyridoxal metabolic process aldehyde metabolic process aldehyde biosynthetic process metabolic compound salvage pyridoxal 5'-phosphate salvage organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound 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	IPR004625	Pyridoxine kinase	Family
A, B, C, D	IPR023685	Pyridoxal kinase PdxY	Family
A, B, C, D	IPR029056	Ribokinase-like	Homologous Superfamily
A, B, C, D	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267
A, B, C, D	MSE	Parent Component: MET RESID: AA0262

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.