3QVG | pdb_00003qvg

XRCC1 bound to DNA ligase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3qvgb1	Alpha and beta proteins (a/b)	BRCT domain	BRCT domain	DNA-repair protein XRCC1	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3qvgb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3qvgd1	Alpha and beta proteins (a/b)	BRCT domain	BRCT domain	DNA-repair protein XRCC1	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3qvgd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3qvgc1	Alpha and beta proteins (a/b)	BRCT domain	BRCT domain	DNA ligase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3qvgc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qvga1	Alpha and beta proteins (a/b)	BRCT domain	BRCT domain	DNA ligase	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3qvga2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	BRCT domain-like	8078192	3000159	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	BRCT domain-like	8078192	3000159	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	BRCT domain-like	8034117	3000159	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BRCT domain-like	8034117	3000159	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	PTCB-BRCT	e3qvgB1	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)
D	PTCB-BRCT	e3qvgD1	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)
C	LIG3_BRCT	e3qvgC1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: LIG3_BRCT	ECOD (1.6)
A	LIG3_BRCT	e3qvgA1	A: a/b three-layered sandwiches	X: BRCT domain (From Topology)	H: BRCT domain (From Topology)	T: BRCT domain	F: LIG3_BRCT	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)
D	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)
C	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)
A	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
B, D	PF16589	BRCT domain (BRCT_2)	BRCT domain	This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general fu ...	This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general function, which remains unknown [1,2].	Domain
A, C	PF16759	DNA ligase 3 BRCT domain (LIG3_BRCT)	DNA ligase 3 BRCT domain	The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerisation [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	DNA repair protein XRCC1	ADP-D-ribose modification-dependent protein binding protein binding binding modification-dependent protein binding poly-ADP-D-ribose binding carbohydrate derivative binding enzyme binding DNA binding oxidized DNA binding damaged DNA binding nucleic acid binding	developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development multicellular organism development central nervous system development anatomical structure development telencephalon development hippocampus development limbic system development developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development multicellular organism development central nervous system development anatomical structure development telencephalon development hippocampus development limbic system development system development cellular response to stimulus response to stimulus single strand break repair 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 base-excision repair regulation of cellular process regulation of cellular response to stress regulation of primary metabolic process regulation of base-excision repair regulation of response to stress regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of DNA repair regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process telomere maintenance in response to DNA damage negative regulation of telomere maintenance negative regulation of biological process telomere organization negative regulation of chromosome organization negative regulation of nucleobase-containing compound metabolic process negative regulation of telomere maintenance in response to DNA damage negative regulation of cellular component organization negative regulation of metabolic process regulation of chromosome organization regulation of organelle organization telomere maintenance telomere capping regulation of telomere maintenance regulation of cellular component organization regulation of protection from non-homologous end joining at telomere cellular component organization negative regulation of cellular process cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of telomere maintenance in response to DNA damage negative regulation of response to stimulus protection from non-homologous end joining at telomere chromosome organization negative regulation of protection from non-homologous end joining at telomere organelle organization negative regulation of organelle organization negative regulation of telomere capping negative regulation of DNA metabolic process regulation of telomere capping response to oxidative stress response to chemical response to oxygen-containing compound response to hydroperoxide double-strand break repair double-strand break repair via nonhomologous end joining DNA recombination mitotic recombination telomeric DNA-containing double minutes formation telomere maintenance via recombination	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle nucleotide-excision repair complex ERCC4-ERCC1 complex membrane-enclosed lumen intracellular membraneless organelle nucleolus membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle nucleotide-excision repair complex ERCC4-ERCC1 complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen chromosome chromosome, telomeric region chromosomal region nucleoplasm chromatin site of DNA damage
A, C	DNA ligase 3	ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity DNA ligase (ATP) activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity DNA ligase (ATP) activity 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 cation binding transition metal ion binding zinc ion binding metal ion binding	DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process regulation of cellular process negative regulation of biological process DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process regulation of cellular process negative regulation of biological process mitochondrial DNA metabolic process regulation of primary metabolic process negative regulation of DNA-templated DNA replication negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of DNA replication negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process mitochondrial DNA replication negative regulation of mitochondrial DNA replication regulation of DNA-templated DNA replication negative regulation of DNA metabolic process regulation of mitochondrial DNA replication negative regulation of mitochondrial DNA metabolic process regulation of metabolic process regulation of mitochondrial DNA metabolic process regulation of DNA metabolic process regulation of DNA replication cell division nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process cellular response to stimulus double-strand break repair response to stimulus DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair base-excision repair mitochondrial DNA repair base-excision repair, gap-filling double-strand break repair via nonhomologous end joining double-strand break repair via alternative nonhomologous end joining cellular component organization organelle organization cellular component organization or biogenesis mitochondrion organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex nucleus nuclear protein-containing complex DNA ligase III-XRCC1 complex membrane-enclosed lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex nucleus nuclear protein-containing complex DNA ligase III-XRCC1 complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
B, D	IPR045080	XRCC1, first (central) BRCT domain	Domain
B, D	IPR001357	BRCT domain	Domain
B, D	IPR002706	DNA-repair protein Xrcc1, N-terminal	Domain
B, D	IPR036420	BRCT domain superfamily	Homologous Superfamily
A, C	IPR036599	DNA ligase, ATP-dependent, N-terminal domain superfamily	Homologous Superfamily
A, C	IPR036957	Zinc finger, PARP-type superfamily	Homologous Superfamily
A, C	IPR001357	BRCT domain	Domain
A, C	IPR012310	DNA ligase, ATP-dependent, central	Domain
A, C	IPR012308	DNA ligase, ATP-dependent, N-terminal	Domain
A, C	IPR036420	BRCT domain superfamily	Homologous Superfamily
A, C	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
A, C	IPR000977	DNA ligase, ATP-dependent	Family
A, C	IPR031916	DNA ligase 3, BRCT domain	Domain
A, C	IPR001510	Zinc finger, PARP-type	Domain
A, C	IPR050191	ATP-dependent DNA ligase	Family
A, C	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, C	IPR012309	DNA ligase, ATP-dependent, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P49916	atypical teratoid rhabdoid tumor large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor spina bifida breast cancer lung cancer non-small cell lung carcinoma psoriasis subependymal giant cell astrocytoma colorectal cancer malignant mesothelioma osteosarcoma rheumatoid arthritis

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.