2DCN | pdb_00002dcn

Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate (alpha-furanose form)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d2dcna1	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	Ribokinase-like	Hypothetical fructokinase ST2478	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
B	d2dcnb_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
C	d2dcnc_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
D	d2dcnd_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
E	d2dcne_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
F	d2dcnf_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
G	d2dcng_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
H	d2dcnh_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
I	d2dcni_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
J	d2dcnj_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
K	d2dcnk_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)
L	d2dcnl_	Alpha and beta proteins (a/b)	Ribokinase-like	Ribokinase-like	automated matches	automated matches	(Sulfurisphaera tokodaii str. 7 ) [TaxId: 273063 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ribokinase-like	8027283	4000759	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribokinase-like	8039662	3001268	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ribokinase-like	8039662	3001268	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PfkB	e2dcnA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
B	PfkB	e2dcnB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
C	PfkB	e2dcnC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
D	PfkB	e2dcnD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
E	PfkB	e2dcnE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
F	PfkB	e2dcnF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
G	PfkB	e2dcnG1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
H	PfkB	e2dcnH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
I	PfkB	e2dcnI1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
J	PfkB	e2dcnJ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
K	PfkB	e2dcnK1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: PfkB	ECOD (1.6)
L	PfkB	e2dcnL1	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)
A	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	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)
C	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
D	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
E	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
F	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
G	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
H	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
I	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
J	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
K	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)
L	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	hypothetical fructokinase	carbohydrate kinase activity kinase activity transferase activity 2-dehydro-3-deoxygluconokinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding carbohydrate kinase activity kinase activity transferase activity 2-dehydro-3-deoxygluconokinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR011611	Carbohydrate kinase PfkB	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR054939	2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR029056	Ribokinase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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.