Annotations: 1Z56

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	XLF-Cernunnos	8044653	4004063	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	XRCC4 C-terminal oligomerization domain-like	8051836	3001502	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	XRCC4 C-terminal oligomerization domain-like	8051836	3001502	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)
C	PTCB-BRCT	e1z56C2	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: PTCB-BRCT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.5.370	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.20.5.370	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00533	BRCA1 C Terminus (BRCT) domain (BRCT)	BRCA1 C Terminus (BRCT) domain	The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- ...	The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs [2]. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode [3]. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ligase interacting factor 1	chromatin binding 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	cellular anatomical structure intracellular anatomical structure cytoplasm 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 cellular anatomical structure intracellular anatomical structure cytoplasm 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 membraneless organelle intracellular membraneless organelle chromatin chromosome
C	DNA ligase IV	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 nucleic acid binding ligase activity, forming phosphoric ester bonds DNA ligase (ATP) activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity cation binding metal ion binding	primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process chromosome organization maintenance of DNA repeat elements primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process chromosome organization maintenance of DNA repeat elements cellular component organization maintenance of rDNA organelle organization cellular component organization or biogenesis cell division double-strand break repair via classical nonhomologous end joining 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 nucleotide-excision repair, DNA gap filling nucleotide-excision repair DNA recombination	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
D	Ligase interacting factor 1	-	-	-
E, H	Ligase interacting factor 1	-	-	-
F	Ligase interacting factor 1	-	-	-
G	Ligase interacting factor 1	-	-	-
I	Ligase interacting factor 1	-	-	-
J	Ligase interacting factor 1	-	-	-
K	Ligase interacting factor 1	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR014751	DNA repair protein XRCC4-like, C-terminal	Homologous Superfamily
C	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
C	IPR000977	DNA ligase, ATP-dependent	Family
C	IPR036599	DNA ligase, ATP-dependent, N-terminal domain superfamily	Homologous Superfamily
C	IPR029710	DNA ligase 4	Family
C	IPR001357	BRCT domain	Domain
C	IPR012310	DNA ligase, ATP-dependent, central	Domain
C	IPR012308	DNA ligase, ATP-dependent, N-terminal	Domain
C	IPR044125	DNA Ligase 4, adenylation domain	Domain
C	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C	IPR036420	BRCT domain superfamily	Homologous Superfamily

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.