5E50 | pdb_00005e50

APLF/XRCC4 complex

External Resource: Annotation

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	SMAD/FHA domain-like	8088232	3000137	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SMAD/FHA domain-like	8088232	3000137	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)
B		e5e50B1	A: a/b three-layered sandwiches	X: CBS-domain	H: Porins	T: Invertebrate chitin-binding proteins	F:	ECOD (v294.1)
A	HATPase_c	e5e50A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: HATPase_c	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.200.20	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
A	2.60.200.20	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17913	FHA domain (FHA_2)	FHA domain	This entry represents a divergent FHA domain which in PNK binds to phosphorylated segment of XRCC1 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Aprataxin and PNK-like factor	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 histone chaperone activity protein carrier 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
C, D	XRCC4	protein binding binding FHA domain binding protein domain specific binding protein-macromolecule adaptor activity molecular adaptor activity DNA binding nucleic acid binding enzyme binding identical protein binding	cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to lithium ion cellular response to lithium ion response to stimulus response to metal ion response to chemical cellular process response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus localization cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to lithium ion cellular response to lithium ion response to stimulus response to metal ion response to chemical cellular process response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to site of double-strand break intracellular protein localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cell cycle cell cycle process positive regulation of molecular function regulation of molecular function regulation of catalytic activity biological regulation positive regulation of catalytic activity positive regulation of ligase activity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair double-strand break repair immune system development multicellular organismal process immunoglobulin production somatic cell DNA recombination multicellular organism development somatic recombination of immunoglobulin gene segments V(D)J recombination anatomical structure development somatic diversification of immune receptors system development developmental process production of molecular mediator of immune response DNA recombination gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins immunoglobulin V(D)J recombination biosynthetic process immune system process somatic diversification of immune receptors via germline recombination within a single locus double-strand break repair via nonhomologous end joining	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nonhomologous end joining complex catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nonhomologous end joining complex catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle intracellular protein-containing complex DNA ligase IV complex DNA repair complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen DNA-dependent protein kinase-DNA ligase 4 complex site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019406	Aprataxin and PNK-like factor, PBZ domain	Domain
A, B	IPR041388	PNK, FHA domain	Domain
A, B	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A, B	IPR039253	Aprataxin and PNK-like factor	Family
C, D	IPR053963	XRCC4, C-terminal domain	Domain
C, D	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily
C, D	IPR009089	XRCC4, N-terminal domain superfamily	Homologous Superfamily
C, D	IPR014751	DNA repair protein XRCC4-like, C-terminal	Homologous Superfamily
C, D	IPR053961	XRCC4, N-terminal domain	Domain
C, D	IPR010585	DNA repair protein XRCC4	Family
C, D	IPR053962	XRCC4, coiled-coil domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8IW19	celiac disease osteosarcoma lung carcinoma vascular disease nicotine dependence
C, D	Pharos: Q13426	short stature, microcephaly, and endocrine dysfunction DNA ligase IV deficiency Chromosome Aberrations pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia astrocytic tumor congestive heart failure isolated growth hormone deficiency type IA malignant mesothelioma microcephalic primordial dwarfism-insulin resistance syndrome pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor malignant colon neoplasm malignant pancreatic neoplasm short stature, microcephaly, and endocrine dysfunction DNA ligase IV deficiency Chromosome Aberrations pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia astrocytic tumor congestive heart failure isolated growth hormone deficiency type IA malignant mesothelioma microcephalic primordial dwarfism-insulin resistance syndrome pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor malignant colon neoplasm malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer psoriasis tuberculosis intellectual disability malignant ependymoma medulloblastoma osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
C, D	TPO	Parent Component: THR RESID: AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047

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.