3S40 | pdb_00003s40

The crystal structure of a diacylglycerol kinases from Bacillus anthracis str. Sterne

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3s40d_	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	automated matches	automated matches	anthrax,anthrax bacterium (Bacillus anthracis str. Sterne ) [TaxId: 260799 ],	SCOPe (2.08)
C	d3s40c_	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	automated matches	automated matches	anthrax,anthrax bacterium (Bacillus anthracis str. Sterne ) [TaxId: 260799 ],	SCOPe (2.08)
B	d3s40b_	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	automated matches	automated matches	anthrax,anthrax bacterium (Bacillus anthracis str. Sterne ) [TaxId: 260799 ],	SCOPe (2.08)
A	d3s40a_	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	automated matches	automated matches	anthrax,anthrax bacterium (Bacillus anthracis str. Sterne ) [TaxId: 260799 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PI3K_C2	e3s40D1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (v294.1)
C	Flavin_Reduct	e3s40C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (v294.1)
B	PCI	e3s40B3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: PCI	ECOD (v294.1)
A	Anemone_cytotox	e3s40A1	A: a/b three-layered sandwiches	X: EF-hand	H: Insect pheromone/odorant-binding proteins	T: Insect pheromone/odorant-binding proteins	F: Anemone_cytotox	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
D	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
C	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
C	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
B	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
B	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
A	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
A	2.60.200.40	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF19279	YegS C-terminal NAD kinase beta sandwich-like domain (YegS_C)	YegS C-terminal NAD kinase beta sandwich-like domain	This entry represents the C-terminal domain found in the YegS protein [1,2]. It is related to the beta sandwich domain of NAD kinases. The structure of YegS reveals a two-domain protein with the active site crevice found between the two domains. The ...	This entry represents the C-terminal domain found in the YegS protein [1,2]. It is related to the beta sandwich domain of NAD kinases. The structure of YegS reveals a two-domain protein with the active site crevice found between the two domains. The C-terminal domain contains 13 beta-strands and two alpha-helices. The likely substrate for YegS is phosphatidylglycerol [1].	Domain
A, B, C, D	PF00781	Diacylglycerol kinase catalytic domain (DAGK_cat)	Diacylglycerol kinase catalytic domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	diacylglycerol kinase	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 kinase activity lipid kinase activity transferase activity ATP-dependent diacylglycerol kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	lipid biosynthetic process primary metabolic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR045540	YegS/DAGK, C-terminal domain	Domain
A, B, C, D	IPR050187	Lipid Phosphate Formation and Regulation	Family
A, B, C, D	IPR017438	Inorganic polyphosphate/ATP-NAD kinase, N-terminal	Homologous Superfamily
A, B, C, D	IPR016064	NAD kinase/diacylglycerol kinase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR005218	Diacylglycerol/lipid kinase	Family
A, B, C, D	IPR001206	Diacylglycerol kinase, catalytic domain	Domain

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.