2KN7 | pdb_00002kn7

Structure of the XPF-single strand DNA complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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 [auth D]	d2kn7d_	All alpha proteins	SAM domain-like	RuvA domain 2-like	Hef domain-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2kn7a_	All alpha proteins	SAM domain-like	RuvA domain 2-like	Hef domain-like	automated matches	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 [auth D]	SCOP2B Superfamily	Helix-hairpin-helix tandem	8036445	3000163	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8036445	3000163	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 [auth D]	Cytochrome_CBB3	e2kn7D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
A	Rhodanese	e2kn7A1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Creatinase/prolidase N-terminal domain	T: Creatinase/prolidase N-terminal domain	F: Rhodanese	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth D]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B], D [auth C]	DNA (5'-D(CPAPGPTPGPGPCPTPGPA)-3')	-	-	-
A, B [auth D]	DNA repair endonuclease XPF	TFIID-class transcription factor complex binding transcription factor binding RNA polymerase binding protein binding binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme binding RNA polymerase II general transcription initiation factor binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity TFIID-class transcription factor complex binding transcription factor binding RNA polymerase binding protein binding binding RNA polymerase II complex binding general transcription initiation factor binding RNA polymerase core enzyme binding enzyme binding RNA polymerase II general transcription initiation factor binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA binding damaged DNA binding nucleic acid binding protein-macromolecule adaptor activity molecular adaptor activity chromatin binding promoter-specific chromatin binding single-stranded DNA endonuclease activity hydrolase activity, acting on ester bonds hydrolase activity identical protein binding single-stranded DNA binding	sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle DNA recombination organelle fission primary metabolic process DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process cellular process metabolic process macromolecule metabolic process 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 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 response to stress response to stress regulation of response to stress negative regulation of cellular process 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 biological regulation chromosome organization regulation of macromolecule metabolic process negative regulation of protection from non-homologous end joining at telomere negative regulation of organelle organization DNA damage response negative regulation of telomere capping negative regulation of DNA metabolic process regulation of telomere capping response to light stimulus response to radiation response to abiotic stimulus response to UV UV protection mitotic recombination telomeric DNA-containing double minutes formation telomere maintenance via recombination nucleotide-excision repair involved in interstrand cross-link repair nucleotide-excision repair interstrand cross-link repair DNA repair double-strand break repair recombinational repair double-strand break repair via homologous recombination cellular response to radiation cellular response to environmental stimulus cellular response to light stimulus cellular response to abiotic stimulus cellular response to UV negative regulation of telomere maintenance via telomere lengthening telomere maintenance via telomere lengthening regulation of telomere maintenance via telomere lengthening catabolic process autophagy regulation of catabolic process regulation of autophagy process utilizing autophagic mechanism 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 organelle lumen nucleoplasm 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 organelle lumen nucleoplasm organelle lumen nuclear lumen nucleotide-excision repair factor 1 complex membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B [auth D]	IPR006167	DNA repair protein XPF	Family
A, B [auth D]	IPR010994	RuvA domain 2-like	Homologous Superfamily
A, B [auth D]	IPR006166	ERCC4 domain	Domain
A, B [auth D]	IPR047520	DNA repair endonuclease XPF, nuclease domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth D]	Pharos: Q92889	xeroderma pigmentosum Fanconi anemia Fanconi anemia complementation group Q XFE progeroid syndrome xeroderma pigmentosum group F Arsenic Poisoning germ cell tumor urinary bladder cancer peripheral nervous system disease Cockayne syndrome embryonal neoplasm peripheral neuropathy gastric cancer squamous cell carcinoma hematopoietic and lymphoid system neoplasm xeroderma pigmentosum Fanconi anemia Fanconi anemia complementation group Q XFE progeroid syndrome xeroderma pigmentosum group F Arsenic Poisoning germ cell tumor urinary bladder cancer peripheral nervous system disease Cockayne syndrome embryonal neoplasm peripheral neuropathy gastric cancer squamous cell carcinoma hematopoietic and lymphoid system neoplasm inherited disease susceptibility malignant ependymoma aplastic anemia malignant pancreatic neoplasm Cockayne syndrome type 1 osteosarcoma pancreatic ductal adenocarcinoma gastric carcinoma testicular cancer hepatocellular carcinoma intellectual disability melanoma congenital anemia ovarian carcinoma diabetes mellitus esophageal atresia/tracheoesophageal fistula psoriasis skin basal cell carcinoma glioblastoma urinary bladder neoplasm inherited aplastic anemia large cell medulloblastoma xeroderma pigmentosum-Cockayne syndrome complex attention deficit hyperactivity disorder, inattentive type neurofibromatosis type 1 cutaneous melanoma ovarian neoplasm exocrine pancreatic carcinoma

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.