1RK2

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1rk2a_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1rk2b_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1rk2d_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1rk2c_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	(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)
A	SCOP2B Superfamily	Ribokinase-like	8032756	3001268	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8032756	3001268	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribokinase-like	8032756	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8032756	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)
A	PfkB	e1rk2A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
B	PfkB	e1rk2B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
D	PfkB	e1rk2D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
C	PfkB	e1rk2C1	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)
A	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00294	pfkB family carbohydrate kinase (PfkB)	pfkB family carbohydrate kinase	This family includes a variety of carbohydrate and pyrimidine kinases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RIBOKINASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding carbohydrate kinase activity kinase activity ribokinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups identical protein binding protein binding protein homodimerization activity protein dimerization activity cation binding metal ion binding	monosaccharide metabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic process primary metabolic process organic substance metabolic process small molecule metabolic process metabolic process pentose metabolic process monosaccharide catabolic process small molecule catabolic process pentose catabolic process organic substance catabolic process D-ribose metabolic process monosaccharide metabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic process primary metabolic process organic substance metabolic process small molecule metabolic process metabolic process pentose metabolic process monosaccharide catabolic process small molecule catabolic process pentose catabolic process organic substance catabolic process D-ribose metabolic process D-ribose catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011611	Carbohydrate kinase PfkB	Domain
A, B, C, D	IPR002173	Carbohydrate/purine kinase, PfkB, conserved site	Conserved Site
A, B, C, D	IPR011877	Ribokinase	Family
A, B, C, D	IPR029056	Ribokinase-like	Homologous Superfamily
A, B, C, D	IPR002139	Ribokinase/fructokinase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	ribokinase M-CSA #663	Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. The reaction is the first step in ribose metabolism and acts partly to trap ribose within the cell after uptake. Phosphorylation also prepares the sugar for use in the synthesis of nucleotides, histidine and for entry into the pentose phosphate pathway. Ribokinase is apart of the Ribokinase superfamily (also known as the PfkB family) alongside fructokinase and adenosine kinase which share two conserved motifs at the N and C terminus.	Defined by 4 residues: ALA:A-252ALA:A-253GLY:A-254ASP:A-255 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.1.15 (PDB Primary Data) Search M-CSA Motif + EC 2.7.1.15

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.