5E50

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)
A	SCOP2B Superfamily	SMAD/FHA domain-like	8088232	3000137	SCOP2B (2022-06-29)
B	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)
A	PF17913	e5e50A1	A: beta sandwiches	X: SMAD/FHA domain (From Topology)	H: SMAD/FHA domain (From Topology)	T: SMAD/FHA domain	F: PF17913	ECOD (1.6)
B	PF17913	e5e50B1	A: beta sandwiches	X: SMAD/FHA domain (From Topology)	H: SMAD/FHA domain (From Topology)	T: SMAD/FHA domain	F: PF17913	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.200.20	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)
B	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
C, D	PF06632	DNA double-strand break repair and V(D)J recombination protein XRCC4 (XRCC4)	DNA double-strand break repair and V(D)J recombination protein XRCC4	-	Family

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 organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid protein binding binding histone binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity protein carrier chaperone histone chaperone activity molecular carrier activity 3'-5' exonuclease 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 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 protein-containing complex organization protein-DNA complex organization cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis protein localization cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA repair-dependent chromatin remodeling protein-containing complex organization protein-DNA complex organization cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis protein localization localization protein localization to chromatin cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule 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 organic substance biosynthetic process 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 cellular metabolic process DNA recombination regulation of cellular metabolic process primary metabolic process DNA metabolic process regulation of B cell mediated immunity immune effector process somatic diversification of immunoglobulins regulation of gene expression organic cyclic compound metabolic process 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 cellular biosynthetic process 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 organic substance metabolic process regulation of immunoglobulin mediated immune response leukocyte activation involved in immune response regulation of B cell activation 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 cellular biosynthetic 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 positive regulation of biological process DNA ligation positive regulation of metabolic process regulation of DNA ligation positive regulation of DNA ligation positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of DNA metabolic process double-strand break repair double-strand break repair via nonhomologous end joining	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity 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 intracellular non-membrane-bounded organelle site of DNA damage chromosome non-membrane-bounded organelle
C, D	XRCC4	protein binding binding FHA domain binding protein domain specific binding identical protein binding	cellular response to stimulus cellular response to inorganic substance cellular response to metal ion cellular response to lithium ion response to stimulus response to inorganic substance cellular response to chemical stimulus response to lithium ion response to metal ion response to chemical cellular process positive regulation of molecular function regulation of molecular function regulation of ligase activity cellular response to stimulus cellular response to inorganic substance cellular response to metal ion cellular response to lithium ion response to stimulus response to inorganic substance cellular response to chemical stimulus response to lithium ion response to metal ion response to chemical cellular process positive regulation of molecular function regulation of molecular function regulation of ligase activity regulation of catalytic activity biological regulation positive regulation of catalytic activity positive regulation of ligase activity response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus DNA ligation involved in DNA repair primary metabolic process DNA metabolic process nucleic acid metabolic process DNA ligation nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair protein localization localization cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to site of double-strand break double-strand break repair immune system development multicellular organismal process immunoglobulin production cellular biosynthetic process somatic cell DNA recombination multicellular organism development V(D)J recombination somatic recombination of immunoglobulin gene segments anatomical structure development organic substance biosynthetic process somatic diversification of immune receptors system development developmental process production of molecular mediator of immune response DNA recombination cellular metabolic process 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	protein-containing complex nonhomologous end joining complex catalytic complex intracellular protein-containing complex DNA repair complex membrane-bounded organelle intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle DNA-dependent protein kinase-DNA ligase 4 complex protein-containing complex nonhomologous end joining complex catalytic complex intracellular protein-containing complex DNA repair complex membrane-bounded organelle intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle DNA-dependent protein kinase-DNA ligase 4 complex cytoplasm cytosol DNA ligase IV complex site of double-strand break intracellular non-membrane-bounded organelle site of DNA damage chromosome non-membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

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	IPR014751	DNA repair protein XRCC4-like, C-terminal	Homologous Superfamily
C, D	IPR010585	DNA repair protein XRCC4	Family
C, D	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily
C, D	IPR009089	XRCC4, N-terminal domain superfamily	Homologous Superfamily

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 R01GM133198.