6K78 | pdb_00006k78

Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
B	d6k78b1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
D	d6k78d1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
C	d6k78c1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
A	d6k78a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	C1-set	e6k78B1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
D	C1-set	e6k78D1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
C	C1-set	e6k78C1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
A	C1-set	e6k78A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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
A	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	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
B, C, D	Glycerol 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 kinase activity glycerol kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	carbohydrate metabolic process polyol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process glycerol metabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process phosphate-containing compound metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process phosphorus metabolic process carbohydrate metabolic process polyol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process glycerol metabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process phosphate-containing compound metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process phosphorus metabolic process alcohol catabolic process catabolic process polyol catabolic process carbohydrate catabolic process alditol catabolic process glycerol catabolic process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A	Glycerol 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 kinase activity glycerol kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	carbohydrate metabolic process polyol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process glycerol metabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process phosphate-containing compound metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process phosphorus metabolic process carbohydrate metabolic process polyol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process glycerol metabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process phosphate-containing compound metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process phosphorus metabolic process alcohol catabolic process catabolic process polyol catabolic process carbohydrate catabolic process alditol catabolic process glycerol catabolic process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, C, D	IPR018485	Carbohydrate kinase FGGY, C-terminal	Domain
B, C, D	IPR005999	Glycerol kinase	Family
B, C, D	IPR018483	Carbohydrate kinase, FGGY, conserved site	Conserved Site
B, C, D	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
B, C, D	IPR000577	Carbohydrate kinase, FGGY	Family
B, C, D	IPR018484	Carbohydrate kinase FGGY, N-terminal	Domain
A	IPR018485	Carbohydrate kinase FGGY, C-terminal	Domain
A	IPR005999	Glycerol kinase	Family
A	IPR018483	Carbohydrate kinase, FGGY, conserved site	Conserved Site
A	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A	IPR000577	Carbohydrate kinase, FGGY	Family
A	IPR018484	Carbohydrate kinase FGGY, N-terminal	Domain

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.