1BE4 | pdb_00001be4

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)
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)
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)

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	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)
B	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)
A		e1be4A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
C		e1be4C1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
B		e1be4B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)

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)
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)

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	kinase activity farnesyl diphosphate kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups binding nucleoside phosphate binding ion binding anion binding succinyl-CoA binding heterocyclic compound binding acyl-CoA binding small molecule binding kinase activity farnesyl diphosphate kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups binding nucleoside phosphate binding ion binding anion binding succinyl-CoA binding heterocyclic compound binding acyl-CoA binding small molecule binding sulfur compound binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity cation binding magnesium ion binding metal ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding carbohydrate derivative binding ribonucleotide binding DNA binding nucleic acid binding ADP binding guanyl nucleotide binding GDP binding guanyl ribonucleotide binding coenzyme A binding acetyl-CoA binding nucleobase-containing compound kinase activity nucleoside diphosphate kinase activity catalytic activity, acting on a protein protein kinase activity phosphotransferase activity, nitrogenous group as acceptor phosphotransferase activity, alcohol group as acceptor protein histidine kinase activity identical protein binding protein binding ribonucleoprotein complex binding protein-containing complex binding ribosomal small subunit binding ribosome binding	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process developmental process cellular developmental process catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process developmental process cellular developmental process cell differentiation cellular component organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis 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 ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process ITP biosynthetic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process ITP metabolic process purine nucleotide biosynthetic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process regulation of biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process regulation of fatty acid biosynthetic process regulation of fatty acid metabolic process regulation of lipid biosynthetic process monocarboxylic acid metabolic process regulation of metabolic process lipid metabolic process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development pyrimidine nucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process pyrimidine ribonucleotide metabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate 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 regulation of body fluid levels secretion mammary gland development gland development animal organ development body fluid secretion lactation regulation of biological quality cellular component disassembly cell death execution phase of apoptosis apoptotic DNA fragmentation cellular component disassembly involved in execution phase of apoptosis apoptotic nuclear changes apoptotic process programmed cell death isoprenoid metabolic process organophosphate catabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process acetyl-CoA metabolic process sulfur compound catabolic process acyl-CoA metabolic process sulfur compound metabolic process acetyl-CoA catabolic process CTP biosynthetic process CTP metabolic process nucleoside diphosphate 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.