2HVD | pdb_00002hvd

Human nucleoside diphosphate kinase A complexed with ADP

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	d2hvda_	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	d2hvdb_	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	d2hvdc_	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	SCOP2 Family	Nucleoside diphosphate kinase, NDK	8030070	4001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside diphosphate kinase, NDK	8042449	3001175	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8042449	3001175	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8042449	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		e2hvdA1	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)
B		e2hvdB1	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		e2hvdC1	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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	Nucleoside diphosphate kinase A	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 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 kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 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 DNA binding nucleic acid binding ADP binding nucleobase-containing compound kinase activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity identical protein binding protein binding farnesyl diphosphate kinase activity succinyl-CoA binding acyl-CoA binding sulfur compound binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity RNA binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity cation binding magnesium ion binding metal ion binding guanyl nucleotide binding GDP binding guanyl ribonucleotide binding coenzyme A binding acetyl-CoA binding 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 ribonucleoprotein complex binding protein-containing complex binding ribosomal small subunit binding ribosome binding	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process regulation of biological process regulation of cellular process catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation apoptotic process regulation of programmed cell death cell death programmed cell death ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process ITP biosynthetic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process ITP metabolic process purine nucleotide biosynthetic process developmental process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development pyrimidine nucleotide metabolic process pyrimidine ribonucleoside triphosphate biosynthetic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine-containing compound biosynthetic process pyrimidine ribonucleotide metabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process pyrimidine ribonucleoside triphosphate metabolic process UTP biosynthetic process UTP metabolic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process regulation of body fluid levels secretion transport mammary gland development gland development animal organ development establishment of localization body fluid secretion localization lactation regulation of biological quality isoprenoid metabolic process lipid metabolic process cellular developmental process cell differentiation 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 import into cell endocytosis vesicle-mediated transport 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 oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process regulation of biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process regulation of fatty acid biosynthetic process regulation of fatty acid metabolic process regulation of lipid biosynthetic process monocarboxylic acid metabolic process regulation of metabolic process negative regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process GTP metabolic process GTP biosynthetic process cellular component disassembly execution phase of apoptosis apoptotic DNA fragmentation cellular component disassembly involved in execution phase of apoptosis apoptotic nuclear changes organophosphate catabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process acetyl-CoA metabolic process sulfur compound catabolic process acyl-CoA metabolic process sulfur compound metabolic process acetyl-CoA catabolic process CTP biosynthetic process CTP metabolic process nucleoside diphosphate metabolic process	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol ruffle cell leading edge plasma membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P15531	hypertrophic cardiomyopathy neuroblastoma Neoplasm Metastasis colorectal cancer colorectal carcinoma diabetes mellitus non-small cell lung carcinoma heart disease lung adenocarcinoma congestive heart failure hepatocellular carcinoma neuroblastoma, susceptibility to

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.