1S57

crystal structure of nucleoside diphosphate kinase 2 from Arabidopsis

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	d1s57a_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d1s57b_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d1s57c_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d1s57d_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
E	d1s57e_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
F	d1s57f_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	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	8029931	4001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside diphosphate kinase NDK	8042310	3001175	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8042310	3001175	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8042310	3001175	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8042310	3001175	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8042310	3001175	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleoside diphosphate kinase NDK	8042310	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	NDK	e1s57A1	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases (From Topology)	T: Nucleoside diphosphate kinases	F: NDK	ECOD (1.6)
B	NDK	e1s57B1	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	e1s57C1	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases (From Topology)	T: Nucleoside diphosphate kinases	F: NDK	ECOD (1.6)
D	NDK	e1s57D1	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases (From Topology)	T: Nucleoside diphosphate kinases	F: NDK	ECOD (1.6)
E	NDK	e1s57E1	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases (From Topology)	T: Nucleoside diphosphate kinases	F: NDK	ECOD (1.6)
F	NDK	e1s57F1	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)
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 II	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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	cellular response to stimulus response to light stimulus cellular response to red or far red light regulation of cellular process response to stimulus signaling response to red or far red light detection of abiotic stimulus cell communication cellular response to environmental stimulus cellular response to light stimulus signal transduction phototransduction detection of light stimulus cellular response to stimulus response to light stimulus cellular response to red or far red light regulation of cellular process response to stimulus signaling response to red or far red light detection of abiotic stimulus cell communication cellular response to environmental stimulus cellular response to light stimulus signal transduction phototransduction detection of light stimulus detection of external stimulus regulation of biological process red or far-red light signaling pathway biological regulation response to external stimulus cellular response to radiation detection of stimulus red, far-red light phototransduction cellular process response to radiation response to abiotic stimulus cellular response to abiotic stimulus response to UV ribose phosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process organic substance metabolic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process organic substance biosynthetic 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 organonitrogen compound metabolic process pyrimidine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process organic cyclic compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound 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 phosphorylation CTP biosynthetic process CTP metabolic process response to hydrogen peroxide response to oxidative stress response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species response to inorganic substance auxin-activated signaling pathway response to organic substance response to endogenous stimulus hormone-mediated signaling pathway cellular response to auxin stimulus response to auxin cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone cellular response to organic substance cellular response to hormone stimulus	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle plastid stroma chloroplast stroma chloroplast chloroplast envelope organelle envelope plastid envelope membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle plastid stroma chloroplast stroma chloroplast chloroplast envelope organelle envelope plastid envelope nucleus intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle

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	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
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 National Science Foundation (DBI-1832184), 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 R01GM133198.