3WX8 | pdb_00003wx8

Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila S2 cells

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)
C	d3wx8c_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
B	d3wx8b_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A	d3wx8a_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8035301	3001175	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8035301	3001175	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8035301	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)
C	SusG_C	e3wx8C1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: SusG_C	ECOD (v294.1)
B	SusG_C	e3wx8B1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: SusG_C	ECOD (v294.1)
A	SusG_C	e3wx8A1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: SusG_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	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)
A	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	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	Nucleoside diphosphate kinase	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding magnesium ion binding metal ion binding adenyl ribonucleotide binding adenyl nucleotide binding ATP binding cytoskeletal protein binding microtubule binding protein binding tubulin binding nucleobase-containing compound kinase activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity	nucleoside phosphate metabolic process nucleoside triphosphate biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside phosphate metabolic process nucleoside triphosphate biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process metabolic process cellular process small molecule metabolic process nucleoside triphosphate metabolic process phosphorus metabolic process adherens junction organization cellular component organization cell junction organization cellular component organization or biogenesis cell-cell junction organization cell cycle mitotic cell cycle developmental process multicellular organism development multicellular organismal process anatomical structure development respiratory system development open tracheal system development system development epithelium development morphogenesis of follicular epithelium morphogenesis of an epithelium establishment or maintenance of cell polarity tissue development tissue morphogenesis anatomical structure morphogenesis establishment or maintenance of polarity of follicular epithelium epithelial cell migration, open tracheal system epithelium migration tissue migration ameboidal-type cell migration epithelial cell migration cell migration cell motility regulation of tube architecture, open tracheal system biological regulation regulation of biological quality 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 nucleotide metabolic process pyrimidine ribonucleoside triphosphate metabolic process UTP biosynthetic 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 nucleotide metabolic process purine nucleoside triphosphate biosynthetic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine-containing compound metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process CTP biosynthetic process CTP metabolic process microtubule-based process deoxyribonucleoside triphosphate biosynthetic process deoxyribonucleoside triphosphate metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane polymeric cytoskeletal fiber nucleus intracellular membraneless organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane polymeric cytoskeletal fiber nucleus intracellular membraneless organelle cytoskeleton membraneless organelle nuclear microtubule supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
A, B, C	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B, C	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A, B, C	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.