5KK8 | pdb_00005kk8

Crystal structure of Nucleoside Diphosphate Kinase from Schistosoma mansoni in complex with ADP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d5kk8a1	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	automated matches	Blood fluke (Schistosoma mansoni ) [TaxId: 6183 ],	SCOPe (2.08)
A	d5kk8a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Blood fluke (Schistosoma mansoni ) [TaxId: 6183 ],	SCOPe (2.08)
B	d5kk8b1	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	automated matches	Blood fluke (Schistosoma mansoni ) [TaxId: 6183 ],	SCOPe (2.08)
B	d5kk8b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Blood fluke (Schistosoma mansoni ) [TaxId: 6183 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e5kk8A1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T:	F:	ECOD (20:10:01)
B		e5kk8B1	A: Four-helical up-and-down bundle	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T:	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)
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	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	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 ADP 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 identical protein binding protein binding	carbohydrate derivative metabolic process nucleoside biosynthetic process nucleobase-containing compound metabolic process metabolic compound salvage nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process small molecule metabolic process purine ribonucleoside metabolic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process purine-containing compound salvage small molecule biosynthetic process nucleoside salvage purine ribonucleoside biosynthetic process carbohydrate derivative metabolic process nucleoside biosynthetic process nucleobase-containing compound metabolic process metabolic compound salvage nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process small molecule metabolic process purine ribonucleoside metabolic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process purine-containing compound salvage small molecule biosynthetic process nucleoside salvage purine ribonucleoside biosynthetic process primary metabolic process ribonucleoside biosynthetic process nucleobase-containing compound biosynthetic process nucleoside metabolic process nucleobase-containing small molecule biosynthetic process purine-containing compound metabolic process purine ribonucleoside salvage biosynthetic process purine nucleoside biosynthetic process metabolic process cellular process purine nucleoside metabolic process ribonucleoside metabolic process ribose phosphate metabolic process nucleotide biosynthetic process pyrimidine nucleotide metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process phosphate-containing compound metabolic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process nucleotide metabolic process ribonucleoside triphosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process UTP biosynthetic process nucleoside triphosphate metabolic process UTP metabolic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process 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 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 ribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process nucleotide salvage purine nucleotide salvage CTP biosynthetic process CTP metabolic process deoxyribonucleoside triphosphate biosynthetic process deoxyribonucleoside triphosphate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A, B	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.