1ZS6 | pdb_00001zs6

structure of human nucleoside-diphosphate kinase 3

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1zs6b_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d1zs6d_	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1zs6a1	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	Nucleoside diphosphate kinase, NDK	human (Homo sapiens ) [TaxId: 9606 ],	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	8036217	3001175	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8036217	3001175	SCOP2B (2022-06-29)
A	SCOP2 Family	Nucleoside diphosphate kinase, NDK	8023837	4001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside diphosphate kinase, NDK	8036217	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)
B		e1zs6B1	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 [auth D]		e1zs6D1	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)
A		e1zs6A1	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)
B	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
C [auth D]	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D]	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 [auth D]	Nucleoside diphosphate kinase 3	ion binding binding anion binding phosphatidic acid binding phospholipid binding lipid binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding ion binding binding anion binding phosphatidic acid binding phospholipid binding lipid binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ADP binding guanyl nucleotide binding GDP binding guanyl ribonucleotide binding cyclic nucleotide binding cAMP binding protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity mitochondrion-mitochondrion outer membrane tether activity 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	organelle fusion cellular component organization organelle organization cellular process mitochondrial fusion cellular component organization or biogenesis mitochondrion organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly apoptotic process organelle fusion cellular component organization organelle organization cellular process mitochondrial fusion cellular component organization or biogenesis mitochondrion organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly apoptotic process cell death programmed cell death membrane organization mitochondrial outer membrane fusion outer mitochondrial membrane organization mitochondrial membrane organization pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside triphosphate biosynthetic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process pyrimidine deoxyribonucleotide biosynthetic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process dTTP biosynthetic process pyrimidine deoxyribonucleoside triphosphate metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process pyrimidine nucleoside triphosphate biosynthetic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process dTTP metabolic process nucleoside triphosphate biosynthetic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process nucleoside triphosphate metabolic process pyrimidine nucleotide biosynthetic process cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process cellular response to stress DNA damage response response to stress macromolecule metabolic process DNA repair ribose phosphate metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process ribonucleoside triphosphate biosynthetic process pyrimidine ribonucleoside triphosphate metabolic process UTP biosynthetic process UTP metabolic 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 CTP biosynthetic process CTP metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol mitochondrial membrane membrane organelle outer membrane organelle envelope bounding membrane of organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol mitochondrial membrane membrane organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane intracellular membraneless organelle cilium plasma membrane bounded cell projection ciliary basal body cell projection microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D]	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
A, B, C [auth D]	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A, B, C [auth D]	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A, B, C [auth D]	IPR001564	Nucleoside diphosphate kinase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C [auth D]	Pharos: Q13232	large cell medulloblastoma tuberculosis ovarian cancer psoriasis

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.