1U0R | pdb_00001u0r

Crystal structure of Mycobacterium tuberculosis NAD kinase

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	d1u0rd_	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d1u0rc_	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1u0rb_	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1u0ra_	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	NAD kinase/diacylglycerol kinase-like	8040639	3001940	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	NAD kinase/diacylglycerol kinase-like	8040639	3001940	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NAD kinase/diacylglycerol kinase-like	8040639	3001940	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	NAD kinase/diacylglycerol kinase-like	8040639	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)
D	Lyase_1	e1u0rD1	A: alpha arrays	X: L-aspartase N-terminal domain-like	H: L-aspartase N-terminal domain-like	T: L-aspartase N-terminal domain-like	F: Lyase_1	ECOD (v295.2)
C	Ldl_recept_b	e1u0rC1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Ldl_recept_b	ECOD (v295.2)
C	Nop	e1u0rC2	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Nop	ECOD (v295.2)
B	Ldl_recept_b	e1u0rB1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Ldl_recept_b	ECOD (v295.2)
B	Abhydrolase_1	e1u0rB2	A: alpha arrays	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: Abhydrolase_1	ECOD (v295.2)
A	Ldl_recept_b	e1u0rA1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Ldl_recept_b	ECOD (v295.2)
A	Nop	e1u0rA2	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Nop	ECOD (v295.2)

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	2.60.200.30	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)
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)
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)

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	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 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 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	nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process NADP+ biosynthetic process nucleotide biosynthetic process purine-containing compound 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 nucleoside phosphate biosynthetic process purine nucleotide biosynthetic process oxoacid metabolic process polyphosphate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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

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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.