5C41

Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5c41a1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5c41a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5c41b1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5c41b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5c41c1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5c41c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5c41d1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5c41d2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	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	8041398	3001268	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribokinase-like	8041398	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	PF00294	e5c41A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF00294	ECOD (1.6)
B	PF00294	e5c41B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF00294	ECOD (1.6)
C	PF00294	e5c41C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF00294	ECOD (1.6)
D	PF00294	e5c41D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PF00294	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)
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)

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 cation binding metal ion binding identical protein binding protein binding	carbohydrate derivative metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process organic substance metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process carbohydrate derivative metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process organic substance metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process generation of precursor metabolites and energy nucleotide metabolic process purine-containing compound metabolic process NADP metabolic process organic cyclic compound metabolic process NADPH regeneration organophosphate metabolic process metabolic process cellular process monosaccharide metabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic 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 membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011877	Ribokinase	Family
A, B, C, D	IPR002139	Ribokinase/fructokinase	Family
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	IPR029056	Ribokinase-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9H477	adrenal cortex carcinoma malignant ependymoma pancreatic ductal adenocarcinoma ulcerative colitis astrocytic tumor nasopharyngeal carcinoma spina bifida bipolar I disorder osteosarcoma tuberculosis

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.