3PNM | pdb_00003pnm

Crystal Structure of E.coli Dha kinase DhaK (H56A)

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	d3pnmd_	Alpha and beta proteins (a/b)	DAK1/DegV-like	DAK1/DegV-like	DAK1	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3pnmc_	Alpha and beta proteins (a/b)	DAK1/DegV-like	DAK1/DegV-like	DAK1	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3pnmb_	Alpha and beta proteins (a/b)	DAK1/DegV-like	DAK1/DegV-like	DAK1	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3pnma_	Alpha and beta proteins (a/b)	DAK1/DegV-like	DAK1/DegV-like	DAK1	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	DAK1/DegV-like	8037867	3000337	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DAK1/DegV-like	8037867	3000337	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DAK1/DegV-like	8037867	3000337	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DAK1/DegV-like	8037867	3000337	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)
D		e3pnmD1	A: F-type ATP synthase subunit b	X: Bacterial cell wall synthesis membrane enzyme MraY-related	H: Bacterial cell wall synthesis membrane enzyme MraY-related	T: Phage_int_SAM_6	F:	ECOD (20:10:01)
C		e3pnmC1	A: F-type ATP synthase subunit b	X: Bacterial cell wall synthesis membrane enzyme MraY-related	H: Bacterial cell wall synthesis membrane enzyme MraY-related	T: Phage_int_SAM_6	F:	ECOD (20:10:01)
B		e3pnmB1	A: F-type ATP synthase subunit b	X: Bacterial cell wall synthesis membrane enzyme MraY-related	H: Bacterial cell wall synthesis membrane enzyme MraY-related	T: Phage_int_SAM_6	F:	ECOD (20:10:01)
A		e3pnmA1	A: F-type ATP synthase subunit b	X: Bacterial cell wall synthesis membrane enzyme MraY-related	H: Bacterial cell wall synthesis membrane enzyme MraY-related	T: Phage_int_SAM_6	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.10440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dihydroxyacetone kinase	CATH (4.3.0)
D	3.30.1180.20	Alpha Beta	2-Layer Sandwich	Hypothetical Protein Tm841	Chain: A	CATH (4.3.0)
C	3.40.50.10440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dihydroxyacetone kinase	CATH (4.3.0)
C	3.30.1180.20	Alpha Beta	2-Layer Sandwich	Hypothetical Protein Tm841	Chain: A	CATH (4.3.0)
B	3.40.50.10440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dihydroxyacetone kinase	CATH (4.3.0)
B	3.30.1180.20	Alpha Beta	2-Layer Sandwich	Hypothetical Protein Tm841	Chain: A	CATH (4.3.0)
A	3.40.50.10440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Dihydroxyacetone kinase	CATH (4.3.0)
A	3.30.1180.20	Alpha Beta	2-Layer Sandwich	Hypothetical Protein Tm841	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02733	Dak1 domain (Dak1)	Dak1 domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity kinase activity glycerone kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups phosphoenolpyruvate-glycerone phosphotransferase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process ketone metabolic process ketone catabolic process metabolic process small molecule metabolic process small molecule catabolic process carbohydrate metabolic process polyol metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process ketone metabolic process ketone catabolic process metabolic process small molecule metabolic process small molecule catabolic process carbohydrate metabolic process polyol metabolic process alcohol catabolic process polyol catabolic process carbohydrate catabolic process primary metabolic process alcohol metabolic process alditol catabolic process glycerol metabolic process glycerol catabolic process monosaccharide metabolic process monosaccharide catabolic process carbohydrate derivative metabolic process glycerol catabolic process to glycerone phosphate organophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process primary alcohol metabolic process carbohydrate phosphorylation phosphorylation	protein-containing complex catalytic complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004006	DhaK domain	Domain
A, B, C, D	IPR012736	Dihydroxyacetone kinase DhaK, subunit 1	Domain
A, B, C, D	IPR050861	Dihydroxyacetone Kinase (DAK)	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.