1NDC | pdb_00001ndc

X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION

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	d1ndca_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	(Dictyostelium discoideum ) [TaxId: 44689 ],	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	8022897	4001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside diphosphate kinase, NDK	8035277	3001175	SCOP2 (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	NDK	e1ndcA1	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)
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	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	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 nucleobase-containing compound kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	regulation of localization regulation of cellular process transport negative regulation of biological process negative regulation of transport vesicle-mediated transport localization negative regulation of secretion regulation of secretion by cell secretion by cell negative regulation of exocytosis negative regulation of cellular process negative regulation of secretion by cell regulation of biological process regulation of localization regulation of cellular process transport negative regulation of biological process negative regulation of transport vesicle-mediated transport localization negative regulation of secretion regulation of secretion by cell secretion by cell negative regulation of exocytosis negative regulation of cellular process negative regulation of secretion by cell regulation of biological process regulation of transport secretion biological regulation export from cell regulation of vesicle-mediated transport establishment of localization regulation of secretion exocytosis regulation of exocytosis cellular process purine deoxyribonucleoside triphosphate biosynthetic process dGDP metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process purine deoxyribonucleoside triphosphate metabolic process carbohydrate derivative metabolic process dGTP metabolic process nucleobase-containing compound metabolic process purine deoxyribonucleoside diphosphate metabolic process purine nucleotide metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process dGTP biosynthetic process from dGDP phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process deoxyribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process dGTP biosynthetic process nucleoside triphosphate biosynthetic process 2'-deoxyribonucleotide metabolic process purine nucleoside diphosphate metabolic process 2'-deoxyribonucleotide biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleoside diphosphate metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process purine deoxyribonucleotide metabolic process nucleoside phosphate biosynthetic process metabolic process purine deoxyribonucleotide biosynthetic process nucleoside triphosphate metabolic process deoxyribonucleoside triphosphate biosynthetic process purine nucleotide biosynthetic process cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization reproductive process asexual reproduction translation gene expression macromolecule biosynthetic process protein biosynthetic process translational elongation macromolecule metabolic process protein metabolic process import into cell regulation of cellular component organization negative regulation of endocytosis negative regulation of pinocytosis regulation of endocytosis negative regulation of cellular component organization regulation of pinocytosis pinocytosis endocytosis biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus ribose phosphate 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 pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process ribonucleoside triphosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process UTP biosynthetic process UTP metabolic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process negative regulation of phagocytosis phagocytosis regulation of phagocytosis GTP metabolic process GTP biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate metabolic process purine ribonucleotide metabolic process cellular response to stimulus signaling G protein-coupled receptor signaling pathway signal transduction cell communication CTP biosynthetic process CTP metabolic process	membrane-bounded organelle intracellular anatomical structure intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle endocytic vesicle cell periphery plasma membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle endocytic vesicle cell periphery plasma membrane membrane endomembrane system secretory granule secretory vesicle membraneless organelle intracellular membraneless organelle ribosome cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

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