3IKH | pdb_00003ikh

Crystal structure of Ribokinase in Complex with ATP and glycerol in the active site from Klebsiella pneumoniae

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)
D	d3ikhd1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Klebsiella pneumoniae subsp. pneumoniae MGH 78578 ) [TaxId: 272620 ],	SCOPe (2.08)
D	d3ikhd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Klebsiella pneumoniae subsp. pneumoniae MGH 78578 ) [TaxId: 272620 ],	SCOPe (2.08)
C	d3ikhc1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Klebsiella pneumoniae subsp. pneumoniae MGH 78578 ) [TaxId: 272620 ],	SCOPe (2.08)
C	d3ikhc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Klebsiella pneumoniae subsp. pneumoniae MGH 78578 ) [TaxId: 272620 ],	SCOPe (2.08)
B	d3ikhb1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Klebsiella pneumoniae subsp. pneumoniae MGH 78578 ) [TaxId: 272620 ],	SCOPe (2.08)
B	d3ikhb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Klebsiella pneumoniae subsp. pneumoniae MGH 78578 ) [TaxId: 272620 ],	SCOPe (2.08)
A	d3ikha1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Klebsiella pneumoniae subsp. pneumoniae MGH 78578 ) [TaxId: 272620 ],	SCOPe (2.08)
A	d3ikha2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Klebsiella pneumoniae subsp. pneumoniae MGH 78578 ) [TaxId: 272620 ],	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	8075347	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8075347	3001268	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8075347	3001268	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribokinase-like	8075347	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	MTHFR	e3ikhD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
C	MTHFR	e3ikhC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
B	MTHFR	e3ikhB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
A	MTHFR	e3ikhA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)

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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Carbohydrate 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 carbohydrate kinase activity kinase activity ribokinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	monosaccharide metabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic process primary metabolic process small molecule metabolic process metabolic process cellular process pentose metabolic process monosaccharide catabolic process small molecule catabolic process pentose catabolic process D-ribose metabolic process D-ribose catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

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

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.