5C3Y | pdb_00005c3y

Structure of human ribokinase crystallized with AMPPNP

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)
L	d5c3yl1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d5c3yl2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d5c3yk1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d5c3yk2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d5c3yj1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d5c3yj2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d5c3yi1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d5c3yi2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5c3yh1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d5c3yh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5c3yg1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5c3yg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5c3yf1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5c3yf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5c3ye1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5c3ye2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5c3yd1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5c3yd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5c3yc1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5c3yc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5c3yb1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5c3yb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5c3ya_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Ribokinase	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)
L	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8041398	3001268	SCOP2B (2022-06-29)
A	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)
L	PfkB	e5c3yL1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
K	PfkB	e5c3yK1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
J	PfkB	e5c3yJ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
I	PfkB	e5c3yI1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
H	PfkB	e5c3yH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
G	PfkB	e5c3yG1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
F	PfkB	e5c3yF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
E	PfkB	e5c3yE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
D	PfkB	e5c3yD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
C	PfkB	e5c3yC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
B	PfkB	e5c3yB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
A	PfkB	e5c3yA1	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)
L	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
K	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
J	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
I	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
H	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
G	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
F	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
E	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)
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, E A, B, C, D, E, F, G, H, I, J, K, L	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, E A, B, C, D, E, F, G, H, I, J, K, L	Ribokinase	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 identical protein binding protein binding	nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process carbohydrate derivative metabolic process primary metabolic process generation of precursor metabolites and energy glucose 6-phosphate metabolic process nucleotide metabolic process NADP+ metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process NADPH regeneration purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process carbohydrate derivative metabolic process primary metabolic process generation of precursor metabolites and energy glucose 6-phosphate metabolic process nucleotide metabolic process NADP+ metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process NADPH regeneration purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic 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 D-ribose metabolic process D-ribose catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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, E A, B, C, D, E, F, G, H, I, J, K, L	IPR011877	Ribokinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR002139	Ribokinase/fructokinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR011611	Carbohydrate kinase PfkB	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR002173	Carbohydrate/purine kinase, PfkB, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR029056	Ribokinase-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

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