3K75 | pdb_00003k75

X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic 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 [auth B]	d3k75b_	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)
B [auth C]	d3k75c_	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)
C [auth D]	d3k75d1	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	DNA polymerase beta-like, second domain	DNA polymerase beta	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth D]	d3k75d2	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	DNA polymerase beta-like	DNA polymerase beta, catalytic (31 kD) fragment	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C [auth D]	d3k75d3	Artifacts	Tags	Tags	Tags	C-terminal Tags	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D [auth E]	d3k75e1	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	DNA polymerase beta-like, second domain	DNA polymerase beta	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D [auth E]	d3k75e2	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	DNA polymerase beta-like	DNA polymerase beta, catalytic (31 kD) fragment	rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	galactose-binding domain-like	8041154	3000087	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	galactose-binding domain-like	8041154	3000087	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Nucleotidyltransferase-like	8042125	3000129	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	PsbU/PolX domain-like	8042124	3000893	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Nucleotidyltransferase-like	8042125	3000129	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	PsbU/PolX domain-like	8042124	3000893	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 [auth B]	Melibiase, Melibiase_2	e3k75B1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: Melibiase, Melibiase_2	ECOD (v294.1)
B [auth C]	Tachylectin	e3k75C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: Tachylectin	ECOD (v294.1)
C [auth D]	Melibiase, Melibiase_2	e3k75D1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: Melibiase, Melibiase_2	ECOD (v294.1)
D [auth E]	Tachylectin	e3k75E1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: Tachylectin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
B [auth C]	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
C [auth D]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C [auth D]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
C [auth D]	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)
D [auth E]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D [auth E]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
D [auth E]	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
C [auth D], D [auth E]	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
C [auth D], D [auth E]	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
C [auth D], D [auth E]	PF10391	Fingers domain of DNA polymerase lambda (DNA_pol_lambd_f)	Fingers domain of DNA polymerase lambda	DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the centr ...	DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth C]	DNA repair protein XRCC1	DNA binding oxidized DNA binding binding damaged DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity 3' overhang single-stranded DNA endonuclease activity DNA endonuclease activity single-stranded DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA DNA binding oxidized DNA binding binding damaged DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity 3' overhang single-stranded DNA endonuclease activity DNA endonuclease activity single-stranded DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity 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	regulation of molecular function regulation of catalytic 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 developmental process multicellular organismal process head development forebrain development animal organ development brain development regulation of molecular function regulation of catalytic 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 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 telomere maintenance in response to DNA damage negative regulation of telomere maintenance regulation of cellular process response to stimulus regulation of cellular response to stress negative regulation of biological process telomere organization regulation of primary metabolic process nucleobase-containing compound 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 primary metabolic process DNA metabolic process regulation of chromosome organization regulation of organelle organization telomere maintenance telomere capping regulation of response to stimulus metabolic process macromolecule metabolic process 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 cellular response to stress response to stress 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 nucleic acid metabolic process organelle organization negative regulation of organelle organization DNA damage response cellular process negative regulation of telomere capping negative regulation of DNA metabolic process regulation of telomere capping DNA recombination mitotic recombination telomeric DNA-containing double minutes formation telomere maintenance via recombination single strand break repair DNA repair base-excision repair regulation of base-excision repair regulation of DNA repair 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	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 nucleoplasm chromatin chromosome chromosome, telomeric region chromosomal region site of DNA damage
C [auth D], D [auth E]	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 damaged DNA binding nucleic acid binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase 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 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 endonuclease activity DNA nuclease activity DNA endonuclease activity nuclease 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 somatic cell DNA recombination somatic recombination of immunoglobulin gene segments V(D)J recombination immunoglobulin heavy chain V-D-J recombination somatic diversification of immune receptors 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 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	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex polymeric cytoskeletal fiber spindle intracellular membraneless organelle spindle microtubule intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber microtubule cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex polymeric cytoskeletal fiber spindle intracellular membraneless organelle spindle microtubule intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth C]	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A [auth B], B [auth C]	IPR045080	XRCC1, first (central) BRCT domain	Domain
A [auth B], B [auth C]	IPR001357	BRCT domain	Domain
A [auth B], B [auth C]	IPR002706	DNA-repair protein Xrcc1, N-terminal	Domain
A [auth B], B [auth C]	IPR036420	BRCT domain superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR010996	Crossover junction endonuclease MUS81-like, HHH domain	Domain
C [auth D], D [auth E]	IPR019843	DNA polymerase family X, binding site	Binding Site
C [auth D], D [auth E]	IPR029398	DNA polymerase beta, thumb domain	Domain
C [auth D], D [auth E]	IPR002008	DNA polymerase family X, beta-like	Family
C [auth D], D [auth E]	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR027421	DNA polymerase lambda lyase domain superfamily	Homologous Superfamily
C [auth D], D [auth E]	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
C [auth D], D [auth E]	IPR028207	DNA polymerase beta, palm domain	Domain
C [auth D], D [auth E]	IPR022312	DNA polymerase family X	Family
C [auth D], D [auth E]	IPR018944	DNA polymerase lambda, fingers domain	Domain
C [auth D], D [auth E]	IPR002054	DNA-directed DNA polymerase X	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], B [auth C]	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.