7Z6O | pdb_00007z6o

X-Ray studies of Ku70/80 reveal the binding site for IP6

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	vWA-like	8035579	3000832	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SPOC domain-like	8035577	3000675	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	vWA-like	8035574	3000832	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SPOC domain-like	8035571	3000675	SCOP2B (2022-06-29)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (utative)
B	1.10.1600.10	Mainly Alpha	Orthogonal Bundle	Ku70	Chain: A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF02735	Ku70/Ku80 beta-barrel domain (Ku)	Ku70/Ku80 beta-barrel domain	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bi ...	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].	Domain
B	PF03730	Ku70/Ku80 C-terminal arm (Ku_C)	Ku70/Ku80 C-terminal arm	-	Family
B	PF03731	Ku70/Ku80 N-terminal alpha/beta domain (Ku_N)	Ku70/Ku80 N-terminal alpha/beta domain	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal ...	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].	Domain
A	PF02735	Ku70/Ku80 beta-barrel domain (Ku)	Ku70/Ku80 beta-barrel domain	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-bi ...	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].	Domain
A	PF03730	Ku70/Ku80 C-terminal arm (Ku_C)	Ku70/Ku80 C-terminal arm	-	Family
A	PF03731	Ku70/Ku80 N-terminal alpha/beta domain (Ku_N)	Ku70/Ku80 N-terminal alpha/beta domain	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal ...	The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	DNA (5'-D(PAPAPAPTPAPAPAPCPTPAPAPAPAPAP*C)-3')	-	-	-
C	DNA (5'-D(GPTPTPTPTPTPAPGPTPTPTPAP*T)-3')	-	-	-
B	X-ray repair cross-complementing protein 5	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA binding U3 snoRNA binding snoRNA binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA binding U3 snoRNA binding snoRNA binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity telomeric DNA 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 protein-containing complex binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding DNA end binding nucleic acid conformation isomerase activity isomerase activity DNA helicase activity helicase activity macromolecular conformation isomerase activity damaged DNA binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process stem cell proliferation cell population proliferation cellular developmental process hemopoiesis cell differentiation anatomical structure development hematopoietic stem cell proliferation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process stem cell proliferation cell population proliferation cellular developmental process hemopoiesis cell differentiation anatomical structure development hematopoietic stem cell proliferation cell development biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus regulation of biological process regulation of cellular process regulation of smooth muscle cell proliferation regulation of cell population proliferation biological regulation muscle cell proliferation smooth muscle cell proliferation localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to chromosome, telomeric region intracellular protein localization positive regulation of nervous system development multicellular organismal process regulation of developmental process positive regulation of biological process regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process multicellular organism development neurogenesis positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of cellular process system development regulation of multicellular organismal development positive regulation of cell development nervous system development positive regulation of multicellular organismal process regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of biological process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription negative regulation of metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus regulation of response to external stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress regulation of immune system process positive regulation of immune system process positive regulation of innate immune response regulation of innate immune response regulation of response to stimulus positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response telomere maintenance via telomerase telomere organization chromosome organization DNA metabolic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis DNA biosynthetic process cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus response to gamma radiation regulation of telomere maintenance regulation of cellular component organization regulation of t-circle formation cellular component biogenesis cellular component assembly negative regulation of cellular component organization formation of extrachromosomal circular DNA regulation of chromosome organization regulation of cellular component biogenesis regulation of organelle organization negative regulation of t-circle formation telomere maintenance via telomere trimming t-circle formation negative regulation of DNA metabolic process regulation of DNA metabolic process DNA recombination stem cell differentiation hematopoietic stem cell differentiation hematopoietic progenitor cell differentiation recombinational repair DNA repair double-strand break repair response to peptide response to chemical response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor double-strand break repair via nonhomologous end joining ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis ribosome biogenesis protein-RNA complex organization cytosolic ribosome assembly protein-containing complex assembly small-subunit processome assembly cytosolic small ribosomal subunit assembly ribosome assembly	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle protein-containing complex organelle nucleus nuclear protein-containing complex Ku70:Ku80 complex intracellular membrane-bounded organelle preribosome cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle protein-containing complex organelle nucleus nuclear protein-containing complex Ku70:Ku80 complex intracellular membrane-bounded organelle preribosome ribonucleoprotein complex small-subunit processome catalytic complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups DNA-dependent protein kinase complex serine/threonine protein kinase complex membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen cell periphery plasma membrane nucleoplasm nonhomologous end joining complex intracellular protein-containing complex DNA repair complex extracellular region DNA-dependent protein kinase-DNA ligase 4 complex vesicle lumen intracellular vesicle cytoplasmic vesicle lumen secretory granule lumen endomembrane system cytoplasmic vesicle secretory granule secretory vesicle vesicle protein-DNA complex telomere cap complex chromosome, telomeric repeat region nuclear telomere cap complex site of DNA damage
A	X-ray repair cross-complementing protein 6	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity ATP-dependent activity, acting on DNA ATP-dependent activity telomeric DNA 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 protein-containing complex binding scaffold protein binding protein binding cyclin binding nucleic acid conformation isomerase activity isomerase activity DNA helicase activity helicase activity macromolecular conformation isomerase activity RNA binding damaged DNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of biological process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of biological process cell population proliferation regulation of cellular process regulation of smooth muscle cell proliferation regulation of cell population proliferation biological regulation muscle cell proliferation cellular process smooth muscle cell proliferation response to X-ray cellular response to stimulus cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus cellular response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation positive regulation of cellular process protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process response to osmotic stress cellular response to salt stress cellular hyperosmotic salinity response cellular response to chemical stress cellular response to osmotic stress response to salt stress hyperosmotic salinity response cellular response to chemical stimulus hyperosmotic response cellular hyperosmotic response cellular response to stress response to chemical regulation of leukocyte differentiation multicellular organismal process cellular developmental process regulation of developmental process regulation of leukocyte activation cell development regulation of cell activation regulation of cell differentiation mononuclear cell differentiation lymphocyte differentiation lymphocyte activation regulation of cell development leukocyte activation positive regulation of developmental process multicellular organism development positive regulation of lymphocyte activation positive regulation of cell activation positive regulation of hemopoiesis positive regulation of cell differentiation cell differentiation anatomical structure development positive regulation of leukocyte activation regulation of immune system process regulation of multicellular organismal process positive regulation of immune system process developmental process regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis cell activation positive regulation of cell development regulation of hemopoiesis positive regulation of multicellular organismal process positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation leukocyte differentiation regulation of lymphocyte activation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus regulation of response to external stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress positive regulation of innate immune response regulation of innate immune response regulation of response to stimulus positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cellular response to gamma radiation response to gamma radiation double-strand break repair via classical nonhomologous end joining double-strand break repair double-strand break repair via nonhomologous end joining DNA metabolic process DNA damage response DNA repair telomere organization chromosome organization telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis DNA recombination recombinational repair	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle organelle nucleus nuclear protein-containing complex Ku70:Ku80 complex intracellular membrane-bounded organelle cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle organelle nucleus nuclear protein-containing complex Ku70:Ku80 complex intracellular membrane-bounded organelle catalytic complex transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups DNA-dependent protein kinase complex serine/threonine protein kinase complex membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen intracellular vesicle ficolin-1-rich granule endomembrane system cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle nucleoplasm nonhomologous end joining complex intracellular protein-containing complex DNA repair complex extracellular region DNA-dependent protein kinase-DNA ligase 4 complex vesicle lumen cytoplasmic vesicle lumen secretory granule lumen protein-DNA complex telomere cap complex chromosome, telomeric repeat region nuclear telomere cap complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR036494	Ku, C-terminal domain superfamily	Homologous Superfamily
B	IPR016194	SPOC-like, C-terminal domain superfamily	Homologous Superfamily
B	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B	IPR002035	von Willebrand factor, type A	Domain
B	IPR005161	Ku70/Ku80, N-terminal alpha/beta	Domain
B	IPR014893	Ku, C-terminal	Domain
B	IPR006164	Ku70/Ku80, DNA-binding domain	Domain
B	IPR005160	Ku70/Ku80 C-terminal arm	Domain
B	IPR024193	Ku80	Family
A	IPR016194	SPOC-like, C-terminal domain superfamily	Homologous Superfamily
A	IPR027388	Ku70, bridge and pillars domain superfamily	Homologous Superfamily
A	IPR036361	SAP domain superfamily	Homologous Superfamily
A	IPR006165	Ku70	Family
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR005161	Ku70/Ku80, N-terminal alpha/beta	Domain
A	IPR006164	Ku70/Ku80, DNA-binding domain	Domain
A	IPR047087	Ku70, core domain	Domain
A	IPR005160	Ku70/Ku80 C-terminal arm	Domain
A	IPR003034	SAP domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P13010	primitive neuroectodermal tumor Adenocarcinoma of Lung atypical teratoid rhabdoid tumor large cell medulloblastoma lupus erythematosus medulloblastoma ovarian cancer systemic lupus erythematosus breast cancer glioblastoma lung adenocarcinoma lymphoplasmacytic lymphoma myopathy plasma cell myeloma breast carcinoma primitive neuroectodermal tumor Adenocarcinoma of Lung atypical teratoid rhabdoid tumor large cell medulloblastoma lupus erythematosus medulloblastoma ovarian cancer systemic lupus erythematosus breast cancer glioblastoma lung adenocarcinoma lymphoplasmacytic lymphoma myopathy plasma cell myeloma breast carcinoma Hodgkins lymphoma lung cancer malignant glioma osteosarcoma
A	Pharos: P12956	Adenocarcinoma of Lung lupus erythematosus systemic lupus erythematosus lymphoplasmacytic lymphoma lung adenocarcinoma 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.