6TYT | pdb_00006tyt

Structure of Ku80 von Willebrand domain S229A mutant complexed with APLF and XLF Ku Binding Motif

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ku_N	e6tytA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Ku_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
C	ARG-LYS-ARG-ILE-LEU-PRO-THR-TRP-MET-LEU-ALA	protein binding binding histone binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity protein binding binding histone binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity protein carrier chaperone histone chaperone activity molecular carrier activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity ADP-D-ribose modification-dependent protein binding modification-dependent protein binding poly-ADP-D-ribose binding carbohydrate derivative binding DNA-(apurinic or apyrimidinic site) endonuclease activity protein folding chaperone cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA repair-dependent chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis localization protein localization to chromatin protein localization to chromosome cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA repair-dependent chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization regulation of epithelial to mesenchymal transition developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation animal organ development regulation of cell differentiation mesenchyme development tissue development epithelial to mesenchymal transition cell differentiation anatomical structure development mesenchymal cell differentiation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process multicellular organismal process regulation of DNA recombination regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response cell activation involved in immune response regulation of primary metabolic process nucleobase-containing compound metabolic process multicellular organism development leukocyte mediated immunity regulation of immune system process somatic diversification of immune receptors regulation of nucleobase-containing compound metabolic process somatic recombination of immunoglobulin genes involved in immune response system development immune response regulation of adaptive immune response DNA recombination primary metabolic process DNA metabolic process regulation of B cell mediated immunity immune effector process somatic diversification of immunoglobulins regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus B cell mediated immunity regulation of immune response regulation of macromolecule biosynthetic process metabolic process regulation of production of molecular mediator of immune response macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process isotype switching immune system development immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination lymphocyte activation leukocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immunoglobulin mediated immune response regulation of B cell activation leukocyte activation involved in immune response regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process production of molecular mediator of immune response regulation of isotype switching B cell activation cell activation regulation of macromolecule metabolic process gene expression adaptive immune response immunoglobulin mediated immune response macromolecule biosynthetic process nucleic acid metabolic process regulation of lymphocyte mediated immunity regulation of immunoglobulin production immune system process somatic diversification of immune receptors via germline recombination within a single locus regulation of lymphocyte activation multi-multicellular organism process reproductive process female pregnancy embryo implantation multi-organism reproductive process single strand break repair DNA repair double-strand break repair double-strand break repair via nonhomologous end joining	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome
B	ALA-LYS-GLY-LEU-PHE-MET	DNA binding binding DNA end binding nucleic acid binding	cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair telomere organization chromosome organization telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis	membrane-bounded organelle protein-containing complex nonhomologous end joining complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle intracellular protein-containing complex DNA ligase IV complex DNA repair complex
A	X-ray repair cross-complementing protein 5	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 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 double-stranded DNA binding nucleic acid binding hydrolase activity catalytic activity ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity ATP-dependent activity sequence-specific DNA binding telomeric DNA binding damaged DNA binding	nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress DNA repair telomere organization chromosome organization telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex Ku70:Ku80 complex intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR019406	Aprataxin and PNK-like factor, PBZ domain	Domain
C	IPR041388	PNK, FHA domain	Domain
C	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
C	IPR039253	Aprataxin and PNK-like factor	Family
B	IPR052287	Non-homologous end-joining factor	Family
B	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily
B	IPR015381	XLF-like, N-terminal	Domain
B	IPR053829	XLF-like, coiled-coil region	Domain
A	IPR036494	Ku, C-terminal domain superfamily	Homologous Superfamily
A	IPR024193	Ku80	Family
A	IPR016194	SPOC-like, C-terminal domain superfamily	Homologous Superfamily
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR005161	Ku70/Ku80, N-terminal alpha/beta	Domain
A	IPR014893	Ku, C-terminal	Domain
A	IPR006164	Ku70/Ku80, DNA-binding domain	Domain
A	IPR005160	Ku70/Ku80 C-terminal arm	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q8IW19	celiac disease osteosarcoma lung carcinoma vascular disease nicotine dependence

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.