1NSK

THE CRYSTAL STRUCTURE OF A HUMAN NUCLEOSIDE DIPHOSPHATE KINASE, NM23-H2

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)
A [auth R]	d1nskr_	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 T]	d1nskt_	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)
E [auth N]	d1nskn_	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)
B [auth L]	d1nskl_	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)
D [auth U]	d1nsku_	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)
F [auth O]	d1nsko_	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)
A [auth R]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
C [auth T]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
E [auth N]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
B [auth L]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
D [auth U]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
F [auth O]	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	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 [auth R]	NDK	e1nskR1	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 [auth T]	NDK	e1nskT1	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 [auth N]	NDK	e1nskN1	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 [auth L]	NDK	e1nskL1	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 [auth U]	NDK	e1nskU1	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 [auth O]	NDK	e1nskO1	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 [auth R]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
C [auth T]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
E [auth N]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
B [auth L]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
D [auth U]	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)
F [auth O]	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 [auth R], B [auth L], C [auth T], D [auth U], E [auth N], A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], F [auth O]	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 [auth R], B [auth L], C [auth T], D [auth U], E [auth N], A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], F [auth O]	NUCLEOSIDE DIPHOSPHATE KINASE	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding G-quadruplex DNA binding binding organic cyclic compound binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding G-quadruplex DNA binding binding organic cyclic compound binding nucleic acid 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 guanyl nucleotide binding GDP binding guanyl ribonucleotide 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 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 cation binding metal ion binding identical protein binding protein binding	regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death cellular response to stimulus regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death cellular response to stimulus integrin-mediated signaling pathway cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation 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 pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic 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 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 biosynthetic process organophosphate metabolic process organophosphate 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 developmental process regulation of developmental process epidermis development anatomical structure development regulation of epidermis development tissue development cell adhesion 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 positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process multicellular organismal process positive regulation of keratinocyte differentiation cellular developmental process regulation of epidermal cell differentiation regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process multicellular organism development positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process epithelium development regulation of multicellular organismal development epidermal cell differentiation animal organ development positive regulation of epidermis development positive regulation of epithelial cell differentiation skin development keratinocyte differentiation positive regulation of multicellular organismal process regulation of keratinocyte differentiation positive regulation of epidermal cell differentiation CTP biosynthetic process CTP metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen ruffle perinuclear region of cytoplasm nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], F [auth O]	IPR023005	Nucleoside diphosphate kinase, active site	Active Site
A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], F [auth O]	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], F [auth O]	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily
A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], F [auth O]	IPR001564	Nucleoside diphosphate kinase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], A [auth R], B [auth L], C [auth T], D [auth U], E [auth N], F [auth O]	Pharos: P22392	colorectal cancer benign mesothelioma Colorectal Neoplasms osteoarthritis susceptibility 1 ovarian neoplasm drug-induced liver injury mesothelioma colorectal carcinoma heart disease osteoarthritis ovarian cancer

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.