3LQC

X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain

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)
A	d3lqca_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	N-terminal domain of xrcc1	N-terminal domain of xrcc1	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)
A	SCOP2B Superfamily	galactose-binding domain-like	8041154	3000087	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotidyltransferase-like	8042125	3000129	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	XRCC1_N	e3lqcA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: XRCC1_N	ECOD (1.6)
B	DNA_pol_B_palm	e3lqcB1	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
B	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
B	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
B	PF14792	DNA polymerase beta palm (DNA_pol_B_palm)	DNA polymerase beta palm	The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA repair protein XRCC1	DNA binding oxidized DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 3' overhang single-stranded DNA endodeoxyribonuclease activity single-stranded DNA endodeoxyribonuclease activity DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA DNA binding oxidized DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 3' overhang single-stranded DNA endodeoxyribonuclease activity single-stranded DNA endodeoxyribonuclease activity DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity ADP-D-ribose modification-dependent protein binding protein binding modification-dependent protein binding poly-ADP-D-ribose binding carbohydrate derivative binding enzyme binding	response to stimulus response to chemical response to xenobiotic stimulus regulation of molecular function regulation of catalytic activity negative regulation of transferase activity biological regulation negative regulation of molecular function negative regulation of catalytic activity regulation of transferase activity negative regulation of protein ADP-ribosylation regulation of protein ADP-ribosylation cellular response to stimulus double-strand break repair response to stimulus response to chemical response to xenobiotic stimulus regulation of molecular function regulation of catalytic activity negative regulation of transferase activity biological regulation negative regulation of molecular function negative regulation of catalytic activity regulation of transferase activity negative regulation of protein ADP-ribosylation regulation of protein ADP-ribosylation cellular response to stimulus double-strand break repair DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process replication-born double-strand break repair via sister chromatid exchange cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair 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 voluntary musculoskeletal movement multicellular organismal movement musculoskeletal movement system process nervous system process neuromuscular process cerebellum morphogenesis hindbrain morphogenesis anatomical structure morphogenesis cerebellum development metencephalon development hindbrain development telomere maintenance in response to DNA damage negative regulation of telomere maintenance regulation of cellular process regulation of cellular response to stress negative regulation of biological process telomere organization regulation of primary metabolic process negative regulation of chromosome organization negative regulation of nucleobase-containing compound metabolic process negative regulation of telomere maintenance in response to DNA damage regulation of nucleobase-containing compound metabolic process regulation of biological process 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 response to stimulus regulation of metabolic process regulation of DNA metabolic process regulation of telomere maintenance regulation of cellular component organization regulation of protection from non-homologous end joining at telomere cellular component organization regulation of response to stress 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 regulation of macromolecule metabolic process 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 single strand break repair positive regulation of biological process positive regulation of single strand break repair positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process regulation of single strand break repair regulation of DNA repair positive regulation of DNA metabolic process mitotic recombination telomeric DNA-containing double minutes formation telomere maintenance via recombination base-excision repair response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus response to oxidative stress response to oxygen-containing compound response to hydroperoxide DNA ligation positive regulation of molecular function regulation of ligase activity regulation of DNA ligation positive regulation of DNA ligation regulation of DNA ligase activity positive regulation of catalytic activity positive regulation of DNA ligase activity positive regulation of ligase activity double-strand break repair via nonhomologous end joining	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle nucleotide-excision repair complex ERCC4-ERCC1 complex membrane-enclosed lumen nucleolus intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle nucleotide-excision repair complex ERCC4-ERCC1 complex membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nucleoplasm protein-DNA complex chromatin chromosome chromosome, telomeric region chromosomal region site of DNA damage
B	DNA polymerase beta	catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cytoskeletal protein binding microtubule binding protein binding tubulin binding DNA-(apurinic or apyrimidinic site) endonuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity enzyme binding cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process developmental process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process developmental process multicellular organismal process gland development animal organ development salivary gland development anatomical structure morphogenesis multicellular organism development gland morphogenesis salivary gland morphogenesis anatomical structure development animal organ morphogenesis exocrine system development system development immune system development lymph node development immune system process hematopoietic or lymphoid organ development multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells immunoglobulin production cellular biosynthetic process somatic cell DNA recombination V(D)J recombination somatic recombination of immunoglobulin gene segments immunoglobulin heavy chain V-D-J recombination somatic diversification of immune receptors 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 somatic diversification of immune receptors via germline recombination within a single locus apoptotic process cell death programmed cell death somatic diversification of immune receptors via somatic mutation somatic hypermutation of immunoglobulin genes pyrimidine dimer repair DNA repair embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development response to alcohol response to chemical response to oxygen-containing compound response to ethanol spleen development regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage signal transduction intrinsic apoptotic signaling pathway neuron apoptotic process base-excision repair response to ionizing radiation response to radiation response to abiotic stimulus response to gamma radiation base-excision repair, gap-filling defense response inflammatory response double-strand break repair double-strand break repair via nonhomologous end joining response to oxygen levels response to hyperoxia response to increased oxygen levels	intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex polymeric cytoskeletal fiber spindle spindle microtubule intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex polymeric cytoskeletal fiber spindle spindle microtubule intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR045080	XRCC1, first (central) BRCT domain	Domain
A	IPR001357	BRCT domain	Domain
A	IPR002706	DNA-repair protein Xrcc1, N-terminal	Domain
A	IPR036420	BRCT domain superfamily	Homologous Superfamily
B	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
B	IPR019843	DNA polymerase family X, binding site	Binding Site
B	IPR029398	DNA polymerase beta, thumb domain	Domain
B	IPR002008	DNA polymerase family X, beta-like	Family
B	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
B	IPR027421	DNA polymerase lambda lyase domain superfamily	Homologous Superfamily
B	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
B	IPR028207	DNA polymerase beta, palm domain	Domain
B	IPR022312	DNA polymerase family X	Family
B	IPR010996	DNA polymerase beta-like, N-terminal domain	Domain
B	IPR018944	DNA polymerase lambda, fingers domain	Domain
B	IPR002054	DNA-directed DNA polymerase X	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P18887	esophageal squamous cell carcinoma mixed glioma prostate cancer spinocerebellar ataxia, autosomal recessive 26 Erythema stomatitis malignant glioma osteosarcoma cancer gastric neoplasm malignant mesothelioma mesothelioma neurodegenerative disease benign mesothelioma childhood acute lymphoblastic leukemia esophageal squamous cell carcinoma mixed glioma prostate cancer spinocerebellar ataxia, autosomal recessive 26 Erythema stomatitis malignant glioma osteosarcoma cancer gastric neoplasm malignant mesothelioma mesothelioma neurodegenerative disease benign mesothelioma childhood acute lymphoblastic leukemia glioma lung carcinoma schizophrenia xeroderma pigmentosum colorectal cancer gastric cancer hereditary diffuse gastric adenocarcinoma medulloblastoma

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.