4C5M

Structure of the pyridoxal kinase from Staphylococcus aureus in complex with AMP-PCP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d4c5mb1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
B	d4c5mb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
C	d4c5mc1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
C	d4c5mc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
D	d4c5md1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
D	d4c5md2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
A	d4c5ma1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
A	d4c5ma2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PfkB	e4c5mB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
C	PfkB	e4c5mC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
D	PfkB	e4c5mD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
A	PfkB	e4c5mA1	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)
C	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)
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	PHOSPHOMETHYLPYRIMIDINE KINASE	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 binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding	phosphorylation phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic hydroxy compound metabolic process thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process thiamine biosynthetic process small molecule metabolic process sulfur compound metabolic process pyrimidine-containing compound biosynthetic process phosphorylation phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic hydroxy compound metabolic process thiamine-containing compound metabolic process vitamin biosynthetic process alcohol metabolic process thiamine metabolic process thiamine biosynthetic process small molecule metabolic process sulfur compound metabolic process pyrimidine-containing compound biosynthetic process primary alcohol biosynthetic process water-soluble vitamin metabolic process pyrimidine-containing compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process vitamin metabolic process sulfur compound biosynthetic process biosynthetic process organic hydroxy compound biosynthetic process 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, B, C, D	IPR004399	Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain	Domain
A, B, C, D	IPR029056	Ribokinase-like	Homologous Superfamily
A, B, C, D	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.