1BE4

NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA

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)
B	d1be4b_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d1be4a_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d1be4c_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8035269	3001175	SCOP2B (2022-06-29)
A	SCOP2 Family	Nucleoside diphosphate kinase, NDK	8022889	4001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside diphosphate kinase, NDK	8035269	3001175	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8035269	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)
B	NDK	e1be4B1	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases (From Topology)	T: Nucleoside diphosphate kinases	F: NDK	ECOD (1.6)
A	NDK	e1be4A1	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases (From Topology)	T: Nucleoside diphosphate kinases	F: NDK	ECOD (1.6)
C	NDK	e1be4C1	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases (From Topology)	T: Nucleoside diphosphate kinases	F: NDK	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
C	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 TRANSFERASE	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound 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 catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity 3'-5' exonuclease activity exonuclease 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 identical protein binding protein binding ribonucleoprotein complex binding protein-containing complex binding ribosomal small subunit binding ribosome binding	developmental process cellular developmental process cell differentiation cellular process localization import into cell transport endocytosis establishment of localization vesicle-mediated transport regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation developmental process cellular developmental process cell differentiation cellular process localization import into cell transport endocytosis establishment of localization vesicle-mediated transport regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation positive regulation of epithelial cell proliferation biological regulation positive regulation of biological process regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of cellular process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process ribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process 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 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 regulation of body fluid levels secretion mammary gland development gland development animal organ development body fluid secretion lactation regulation of biological quality phosphorylation CTP biosynthetic process CTP metabolic process	ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection cellular anatomical structure ruffle membrane plasma membrane region cell projection membrane intracellular anatomical structure cytoplasm ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection cellular anatomical structure ruffle membrane plasma membrane region cell projection membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle nucleus

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.