6QA2 | pdb_00006qa2

R80A MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS

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)
A	d6qa2a_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Mycobacterium tuberculosis H37Ra ) [TaxId: 419947 ],	SCOPe (2.08)
B	d6qa2b_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Mycobacterium tuberculosis H37Ra ) [TaxId: 419947 ],	SCOPe (2.08)
C	d6qa2c_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Mycobacterium tuberculosis H37Ra ) [TaxId: 419947 ],	SCOPe (2.08)
D	d6qa2d_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Mycobacterium tuberculosis H37Ra ) [TaxId: 419947 ],	SCOPe (2.08)
E	d6qa2e_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Mycobacterium tuberculosis H37Ra ) [TaxId: 419947 ],	SCOPe (2.08)
F	d6qa2f_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	automated matches	automated matches	(Mycobacterium tuberculosis H37Ra ) [TaxId: 419947 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Nucleoside diphosphate kinase, NDK	8093483	4001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside diphosphate kinase, NDK	8093484	3001175	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8040024	3001175	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8040024	3001175	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8040024	3001175	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8040024	3001175	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8040024	3001175	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8040024	3001175	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	PolyA_pol	e6qa2A1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: PolyA_pol	ECOD (v294.1)
B	La	e6qa2B1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: La	ECOD (v294.1)
C	La	e6qa2C1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: La	ECOD (v294.1)
D	La	e6qa2D1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: La	ECOD (v294.1)
E	La	e6qa2E1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: La	ECOD (v294.1)
F	La	e6qa2F1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: La	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
B	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
C	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
D	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
E	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
F	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00334	Nucleoside diphosphate kinase (NDK)	Nucleoside diphosphate kinase		Domain

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	Nucleoside diphosphate 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 nuclease activity catalytic activity, acting on a nucleic acid catalytic activity nucleobase-containing compound kinase activity kinase activity transferase activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity transferase activity, transferring phosphorus-containing groups phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity cation binding metal ion binding	nucleoside phosphate 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 phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process ribose phosphate metabolic process nucleoside phosphate 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 phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process UTP biosynthetic process nucleoside triphosphate metabolic process UTP metabolic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process GTP metabolic process GTP biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process CTP biosynthetic process CTP metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing biological process involved in interaction with host biological process involved in symbiotic interaction cellular response to stimulus symbiont-mediated perturbation of host cellular process regulation of cellular process small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction cell communication symbiont-mediated perturbation of host process regulation of intracellular signal transduction intracellular signaling cassette signal transduction symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated perturbation of host Rab small GTPase signal transduction modulation of process of another organism regulation of biological process regulation of signaling symbiont-mediated perturbation of host small GTPase-mediated signal transduction biological regulation regulation of response to stimulus regulation of cell communication symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response	cellular anatomical structure extracellular region intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001564	Nucleoside diphosphate 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.