5AZJ

Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP (with disulfide bridge)

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5azja1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
A	d5azja3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
C	d5azjc1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
C	d5azjc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
B	d5azjb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
B	d5azjb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
D	d5azjd1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	automated matches	automated matches	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)
D	d5azjd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Trypanosoma brucei gambiense ) [TaxId: 31285 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00370	e5azjA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00370	ECOD (1.6)
A	PF02782	e5azjA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF02782	ECOD (1.6)
C	PF00370	e5azjC2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00370	ECOD (1.6)
C	PF02782	e5azjC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF02782	ECOD (1.6)
B	PF00370	e5azjB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00370	ECOD (1.6)
B	PF02782	e5azjB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF02782	ECOD (1.6)
D	PF00370	e5azjD1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00370	ECOD (1.6)
D	PF02782	e5azjD2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF02782	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
D	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, C	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, C	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
B, 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, 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, C	Glycerol kinase	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 kinase activity glycerol kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic substance metabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process carbohydrate metabolic process polyol metabolic process alcohol catabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic substance metabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process carbohydrate metabolic process polyol metabolic process alcohol catabolic process catabolic process organic hydroxy compound metabolic process polyol catabolic process carbohydrate catabolic process primary metabolic process alcohol metabolic process alditol catabolic process glycerol metabolic process alditol metabolic process organic hydroxy compound catabolic process glycerol catabolic process small molecule metabolic process small molecule catabolic process organic substance catabolic process	-
B, D	Glycerol kinase	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 kinase activity glycerol kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic substance metabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process carbohydrate metabolic process polyol metabolic process alcohol catabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process organic substance metabolic process glycerol-3-phosphate metabolic process organophosphate metabolic process carbohydrate derivative metabolic process alditol phosphate metabolic process carbohydrate metabolic process polyol metabolic process alcohol catabolic process catabolic process organic hydroxy compound metabolic process polyol catabolic process carbohydrate catabolic process primary metabolic process alcohol metabolic process alditol catabolic process glycerol metabolic process alditol metabolic process organic hydroxy compound catabolic process glycerol catabolic process small molecule metabolic process small molecule catabolic process organic substance catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

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.