3BBB | pdb_00003bbb

Crystal structure of the NM23-H2 transcription factor complex with dinucleotide d(AG)

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)
F	d3bbbf_	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	d3bbbe_	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	d3bbbd_	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	d3bbbc_	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	d3bbbb_	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	d3bbba_	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)
F	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside diphosphate kinase, NDK	8038962	3001175	SCOP2B (2022-06-29)
A	SCOP2 Family	Nucleoside diphosphate kinase, NDK	8026583	4001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside diphosphate kinase, NDK	8038962	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)
F	RNase_P_Rpp14	e3bbbF1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
E	RNase_P_Rpp14	e3bbbE1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
D	RNase_P_Rpp14	e3bbbD1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
C	RNase_P_Rpp14	e3bbbC1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
B	RNase_P_Rpp14	e3bbbB1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
A	NDK	e3bbbA1	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases	T: Nucleoside diphosphate kinases	F: NDK	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
D	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)
B	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, 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
G, H, I, J	DNA (5'-D(APG)-3')	-	-	-
A, B, C, D, E A, B, C, D, E, F	Nucleoside diphosphate kinase B	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity DNA binding G-quadruplex DNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity DNA binding G-quadruplex DNA binding 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 coenzyme A binding sulfur compound binding nucleobase-containing compound kinase activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity 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 purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process nucleobase-containing compound metabolic 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 primary metabolic 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 metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process ITP metabolic process purine nucleotide biosynthetic 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 lipid metabolic process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation 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 macromolecule metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process 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 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 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 cellular anatomical structure cell leading edge 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 cellular anatomical structure cell leading edge 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, 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	IPR034907	Nucleoside diphosphate kinase-like domain	Domain
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.