3PL2 | pdb_00003pl2

Crystal structure of a 5-keto-2-deoxygluconokinase (NCgl0155, Cgl0158) from Corynebacterium glutamicum ATCC 13032 KITASATO at 1.89 A resolution

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3pl2d_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
C	d3pl2c_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
B	d3pl2b_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)
A	d3pl2a_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Corynebacterium glutamicum ) [TaxId: 1718 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ribokinase-like	8075361	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8075361	3001268	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8075361	3001268	SCOP2B (2022-06-29)
A	SCOP2 Family	Ribokinase-like	8075360	4000759	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribokinase-like	8075361	3001268	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PfkB	e3pl2D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
C	PfkB	e3pl2C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
B	PfkB	e3pl2B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
A	PfkB	e3pl2A1	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)
D	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
D	2.20.150.10	Mainly Beta	Single Sheet	putative 5-dehydro-2- deoxygluconokinase like fold	putative 5-dehydro-2- deoxygluconokinase	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)
C	2.20.150.10	Mainly Beta	Single Sheet	putative 5-dehydro-2- deoxygluconokinase like fold	putative 5-dehydro-2- deoxygluconokinase	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)
B	2.20.150.10	Mainly Beta	Single Sheet	putative 5-dehydro-2- deoxygluconokinase like fold	putative 5-dehydro-2- deoxygluconokinase	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)
A	2.20.150.10	Mainly Beta	Single Sheet	putative 5-dehydro-2- deoxygluconokinase like fold	putative 5-dehydro-2- deoxygluconokinase	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	Sugar kinase, ribokinase family	fructokinase activity carbohydrate kinase activity kinase activity hexokinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011611	Carbohydrate kinase PfkB	Domain
A, B, C, D	IPR029056	Ribokinase-like	Homologous Superfamily
A, B, C, D	IPR030830	5-Dehydro-2-deoxygluconokinase	Family
A, B, C, D	IPR023314	5-Dehydro-2-deoxygluconokinase-like superfamily	Homologous Superfamily
A, B, C, D	IPR050306	PfkB Carbohydrate Kinase	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.