3QDK | pdb_00003qdk

Structural insight on mechanism and diverse substrate selection strategy of ribulokinase

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Gtf3_C	e3qdkD1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Gtf3_C	ECOD (v294.1)
C	PGI	e3qdkC1	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: PGI	ECOD (v294.1)
B		e3qdkB1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F:	ECOD (v294.1)
A	Amidase_2	e3qdkA1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00370	FGGY family of carbohydrate kinases, N-terminal domain (FGGY_N)	FGGY family of carbohydrate kinases, N-terminal domain	This domain adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain.	Domain
A, B, C, D	PF02782	FGGY family of carbohydrate kinases, C-terminal domain (FGGY_C)	FGGY family of carbohydrate kinases, C-terminal domain	This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Ribulokinase	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 transferase activity ribulokinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups D-ribulokinase activity	monosaccharide metabolic process arabinose metabolic process carbohydrate metabolic process catabolic process arabinose catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process L-arabinose catabolic process primary metabolic process L-arabinose catabolic process to D-xylulose 5-phosphate D-xylulose 5-phosphate metabolic process L-arabinose metabolic process organophosphate metabolic process phosphate-containing compound metabolic process monosaccharide metabolic process arabinose metabolic process carbohydrate metabolic process catabolic process arabinose catabolic process carbohydrate catabolic process carbohydrate derivative metabolic process L-arabinose catabolic process primary metabolic process L-arabinose catabolic process to D-xylulose 5-phosphate D-xylulose 5-phosphate metabolic process L-arabinose metabolic process organophosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process pentose metabolic process monosaccharide catabolic process small molecule catabolic process pentose catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018485	Carbohydrate kinase FGGY, C-terminal	Domain
A, B, C, D	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B, C, D	IPR000577	Carbohydrate kinase, FGGY	Family
A, B, C, D	IPR018484	Carbohydrate kinase FGGY, N-terminal	Domain
A, B, C, D	IPR005929	Ribulokinase	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.