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		e3pl2D1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: FAD_binding_4	F:	ECOD (20:10:01)
C		e3pl2C1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: FAD_binding_4	F:	ECOD (20:10:01)
B		e3pl2B1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: FAD_binding_4	F:	ECOD (20:10:01)
A		e3pl2A1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: C1-set	F:	ECOD (20:10:01)

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	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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.