1Z0S

Crystal structure of an NAD kinase from Archaeoglobus fulgidus in complex with ATP

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1z0sa_	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	NAD kinase-like	Inorganic polyphosphate/ATP-NAD kinase PpnK	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
B	d1z0sb_	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	NAD kinase-like	Inorganic polyphosphate/ATP-NAD kinase PpnK	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
C	d1z0sc_	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	NAD kinase-like	Inorganic polyphosphate/ATP-NAD kinase PpnK	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
D	d1z0sd_	Multi-domain proteins (alpha and beta)	NAD kinase/diacylglycerol kinase-like	NAD kinase/diacylglycerol kinase-like	NAD kinase-like	Inorganic polyphosphate/ATP-NAD kinase PpnK	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	NAD kinase-like	8022693	4002957	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	NAD kinase/diacylglycerol kinase-like	8035073	3001940	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	NAD kinase/diacylglycerol kinase-like	8035073	3001940	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NAD kinase/diacylglycerol kinase-like	8035073	3001940	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NAD kinase/diacylglycerol kinase-like	8035073	3001940	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	NAD_kinase_C	e1z0sA1	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: NAD_kinase_C	ECOD (1.6)
A	NAD_kinase_N	e1z0sA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: NAD_kinase_N	ECOD (1.6)
B	NAD_kinase_C	e1z0sB1	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: NAD_kinase_C	ECOD (1.6)
B	NAD_kinase_N	e1z0sB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: NAD_kinase_N	ECOD (1.6)
C	NAD_kinase_C	e1z0sC1	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: NAD_kinase_C	ECOD (1.6)
C	NAD_kinase_N	e1z0sC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: NAD_kinase_N	ECOD (1.6)
D	NAD_kinase_C	e1z0sD1	A: beta sandwiches	X: NAD kinase beta sandwich domain-like (From Topology)	H: NAD kinase beta sandwich domain-like (From Topology)	T: NAD kinase beta sandwich domain-like	F: NAD_kinase_C	ECOD (1.6)
D	NAD_kinase_N	e1z0sD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Phosphofructokinase N-terminal domain	F: NAD_kinase_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
A	2.60.200.30	Mainly Beta	Sandwich	Tumour Suppressor Smad4	Probable inorganic polyphosphate/atp-NAD kinase	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	2.60.200.30	Mainly Beta	Sandwich	Tumour Suppressor Smad4	Probable inorganic polyphosphate/atp-NAD kinase	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	2.60.200.30	Mainly Beta	Sandwich	Tumour Suppressor Smad4	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
D	3.40.50.10330	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)
D	2.60.200.30	Mainly Beta	Sandwich	Tumour Suppressor Smad4	Probable inorganic polyphosphate/atp-NAD kinase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF20143	ATP-NAD kinase C-terminal domain (NAD_kinase_C)	ATP-NAD kinase C-terminal domain	Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases E ...	Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86. This entry represents the C-terminal beta sandwich domain.	Domain
A, B, C, D	PF01513	ATP-NAD kinase N-terminal domain (NAD_kinase)	ATP-NAD kinase N-terminal domain	Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases E ...	Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Probable inorganic polyphosphate/ATP-NAD kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding NAD binding NAD+ kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process primary metabolic process nucleotide metabolic process NAD metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process primary metabolic process nucleotide metabolic process NAD metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process purine nucleotide metabolic process organic substance metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pyridine-containing compound metabolic process small molecule metabolic process pyridine nucleotide metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process purine-containing compound biosynthetic process organic substance biosynthetic process NADP biosynthetic process pyridine nucleotide biosynthetic process pyridine-containing compound biosynthetic process nucleobase-containing compound biosynthetic process NADP metabolic process nicotinamide nucleotide biosynthetic process biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process purine nucleotide biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002504	NAD kinase	Family
A, B, C, D	IPR017438	Inorganic polyphosphate/ATP-NAD kinase, N-terminal	Homologous Superfamily
A, B, C, D	IPR017437	ATP-NAD kinase, PpnK-type, C-terminal	Homologous Superfamily
A, B, C, D	IPR016064	NAD kinase/diacylglycerol kinase-like domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.