1UL1 | pdb_00001ul1

Crystal structure of the human FEN1-PCNA complex

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)
F [auth C]	d1ul1c1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	Proliferating cell nuclear antigen (PCNA)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d1ul1b1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	Proliferating cell nuclear antigen (PCNA)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d1ul1a1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	Proliferating cell nuclear antigen (PCNA)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth Z]	d1ul1z1	All alpha proteins	SAM domain-like	5' to 3' exonuclease, C-terminal subdomain	5' to 3' exonuclease, C-terminal subdomain	Flap endonuclease-1 (Fen-1 nuclease)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth Z]	d1ul1z2	Alpha and beta proteins (a/b)	PIN domain-like	PIN domain-like	5' to 3' exonuclease catalytic domain	Flap endonuclease-1 (Fen-1 nuclease)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth Y]	d1ul1y1	All alpha proteins	SAM domain-like	5' to 3' exonuclease, C-terminal subdomain	5' to 3' exonuclease, C-terminal subdomain	Flap endonuclease-1 (Fen-1 nuclease)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth Y]	d1ul1y2	Alpha and beta proteins (a/b)	PIN domain-like	PIN domain-like	5' to 3' exonuclease catalytic domain	Flap endonuclease-1 (Fen-1 nuclease)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth X]	d1ul1x1	All alpha proteins	SAM domain-like	5' to 3' exonuclease, C-terminal subdomain	5' to 3' exonuclease, C-terminal subdomain	Flap endonuclease-1 (Fen-1 nuclease)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth X]	d1ul1x2	Alpha and beta proteins (a/b)	PIN domain-like	PIN domain-like	5' to 3' exonuclease catalytic domain	Flap endonuclease-1 (Fen-1 nuclease)	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)
F [auth C]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C [auth Z]	SCOP2B Superfamily	PIN domain-like	8032931	3001041	SCOP2B (2022-06-29)
C [auth Z]	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8032928	3000537	SCOP2B (2022-06-29)
B [auth Y]	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8032928	3000537	SCOP2B (2022-06-29)
A [auth X]	SCOP2 Family	5' to 3' exonuclease, C-terminal subdomain	8020548	4001035	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Family	FEN1 catalytic domain-like	8020551	4000504	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	5' to 3' exonuclease, C-terminal subdomain	8032928	3000537	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	PIN domain-like	8032931	3001041	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth C]		e1ul1C1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
E [auth B]		e1ul1B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
D [auth A]		e1ul1A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
C [auth Z]		e1ul1Z1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: IMS_HHH	F:	ECOD (20:10:01)
C [auth Z]		e1ul1Z2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: SNO, Peptidase_S51	F:	ECOD (20:10:01)
B [auth Y]		e1ul1Y1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: IMS_HHH	F:	ECOD (20:10:01)
B [auth Y]		e1ul1Y2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: SNO, Peptidase_S51	F:	ECOD (20:10:01)
A [auth X]		e1ul1X1	A: HhH/H2TH	X: SAM/DNA-glycosylase	H: SAM domain-like	T:	F:	ECOD (20:10:01)
A [auth X]		e1ul1X2	A: Flavodoxin-like	X: HAD domain-related	H: PIN domain-like	T: XPG_N,XPG_I	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth C]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
E [auth B]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
D [auth A]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A], E [auth B], F [auth C]	PF02747	Proliferating cell nuclear antigen, C-terminal domain (PCNA_C)	Proliferating cell nuclear antigen, C-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
D [auth A], E [auth B], F [auth C]	PF00705	Proliferating cell nuclear antigen, N-terminal domain (PCNA_N)	Proliferating cell nuclear antigen, N-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
A [auth X], B [auth Y], C [auth Z]	PF00867	XPG I-region (XPG_I)	XPG I-region	-	Family
A [auth X], B [auth Y], C [auth Z]	PF00752	XPG N-terminal domain (XPG_N)	XPG N-terminal domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth A], E [auth B], F [auth C]	Proliferating cell nuclear antigen	protein-containing complex binding binding hydrolase activity, acting on glycosyl bonds catalytic activity, acting on DNA purine-specific mismatch base pair DNA N-glycosylase activity catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity mismatch base pair DNA N-glycosylase activity protein tyrosine kinase binding protein binding kinase binding protein-containing complex binding binding hydrolase activity, acting on glycosyl bonds catalytic activity, acting on DNA purine-specific mismatch base pair DNA N-glycosylase activity catalytic activity, acting on a nucleic acid hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity mismatch base pair DNA N-glycosylase activity protein tyrosine kinase binding protein binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding identical protein binding chromatin binding DNA binding DNA insertion or deletion binding double-stranded DNA binding mismatched DNA binding dinucleotide insertion or deletion binding nucleic acid binding mismatch repair complex binding MutLalpha complex binding damaged DNA binding histone acetyltransferase binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear estrogen receptor binding DNA polymerase binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process macromolecule metabolic process replication fork processing leading strand elongation DNA strand elongation DNA strand elongation involved in DNA replication ovulation cycle rhythmic process estrous cycle reproductive process multicellular organismal reproductive process cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication epithelium development cellular developmental process cell differentiation tissue development epithelial cell differentiation translesion synthesis nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process regulation of cellular response to stress positive regulation of response to stimulus positive regulation of DNA repair regulation of response to stress regulation of DNA repair regulation of response to stimulus response to ketone response to lipid response to endogenous stimulus response to glucocorticoid response to oxygen-containing compound response to corticosteroid response to hormone response to steroid hormone response to chemical response to dexamethasone response to acid chemical response to nitrogen compound response to L-glutamate response to amino acid cellular response to chemical stimulus cellular response to xenobiotic stimulus response to xenobiotic stimulus nuclear DNA replication telomere organization cell cycle DNA replication mitotic cell cycle telomere maintenance via semi-conservative replication cellular component organization mitotic telomere maintenance via semi-conservative replication cell cycle cellular component organization or biogenesis cell cycle process chromosome organization telomere maintenance organelle organization mitotic cell cycle process negative regulation of biological process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process gene expression regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process chromatin organization gland development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration cellular response to oxidative stress cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV base-excision repair, gap-filling base-excision repair response to metal ion response to cadmium ion response to estradiol	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure membraneless organelle intracellular membraneless organelle chromatin chromosome PCNA complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle enzyme activator complex DNA polymerase processivity factor complex male germ cell nucleus germ cell nucleus membrane-enclosed lumen nuclear replication fork nuclear chromosome intracellular organelle lumen organelle lumen replication fork nuclear lumen chromosome, telomeric region chromosomal region PCNA-p21 complex centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton nucleoplasm endomembrane system organelle envelope nuclear envelope nuclear periphery nuclear lamina nuclear body protein-DNA complex replisome
A [auth X], B [auth Y], C [auth Z]	Flap endonuclease-1	5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity cation binding manganese ion binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding 5'-3' exonuclease activity exonuclease activity DNA binding damaged DNA binding nucleic acid binding magnesium ion binding double-stranded DNA binding RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity RNA endonuclease activity DNA exonuclease activity double-stranded DNA exodeoxyribonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process behavior multicellular organismal process system process learning or memory nervous system process cognition memory positive regulation of organelle organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process cellular component organization positive regulation of cell cycle process cellular component organization or biogenesis cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process regulation of biological process regulation of cell cycle process biological regulation chromosome organization sister chromatid cohesion regulation of chromosome organization positive regulation of sister chromatid cohesion regulation of organelle organization positive regulation of cell cycle positive regulation of chromosome organization organelle organization regulation of sister chromatid cohesion response to light stimulus response to stimulus response to radiation response to abiotic stimulus response to UV UV protection cellular response to stimulus double-strand break repair DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair DNA-templated DNA replication nuclear DNA replication telomere organization cell cycle DNA replication telomere maintenance via semi-conservative replication telomere maintenance base-excision repair, gap-filling base-excision repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen membrane nucleoplasm protein-containing complex chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A], E [auth B], F [auth C]	IPR046938	DNA clamp superfamily	Homologous Superfamily
D [auth A], E [auth B], F [auth C]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
D [auth A], E [auth B], F [auth C]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
D [auth A], E [auth B], F [auth C]	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
D [auth A], E [auth B], F [auth C]	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
A [auth X], B [auth Y], C [auth Z]	IPR023426	Flap endonuclease 1	Family
A [auth X], B [auth Y], C [auth Z]	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A [auth X], B [auth Y], C [auth Z]	IPR019974	XPG conserved site	Conserved Site
A [auth X], B [auth Y], C [auth Z]	IPR006084	XPG/Rad2 endonuclease	Family
A [auth X], B [auth Y], C [auth Z]	IPR006086	XPG-I domain	Domain
A [auth X], B [auth Y], C [auth Z]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A [auth X], B [auth Y], C [auth Z]	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A [auth X], B [auth Y], C [auth Z]	IPR006085	XPG, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth A], E [auth B], F [auth C]	Pharos: P12004	psoriasis ataxia-telangiectasia-like disorder 2 hepatoblastoma adenocarcinoma malignant colon neoplasm granular cell carcinoma Radiation Injuries, Experimental tubular adenocarcinoma focal segmental glomerulosclerosis endometriosis pancreatic intraductal papillary-mucinous neoplasm glioblastoma primitive neuroectodermal tumor pustulosis palmaris et plantaris Sjogren syndrome psoriasis ataxia-telangiectasia-like disorder 2 hepatoblastoma adenocarcinoma malignant colon neoplasm granular cell carcinoma Radiation Injuries, Experimental tubular adenocarcinoma focal segmental glomerulosclerosis endometriosis pancreatic intraductal papillary-mucinous neoplasm glioblastoma primitive neuroectodermal tumor pustulosis palmaris et plantaris Sjogren syndrome large cell medulloblastoma astrocytic tumor lung cancer nasopharyngeal carcinoma colonic neoplasm neurodegenerative disease dermatomyositis ovarian cancer pituitary cancer IgA glomerulonephritis ischemic disease lung adenocarcinoma ataxia-telangiectasia-like disorder atypical teratoid rhabdoid tumor malignant glioma brain cancer medulloblastoma breast cancer cribriform carcinoma non-small cell lung carcinoma ductal breast carcinoma in situ pancreatic intraductal papillary-mucinous carcinoma invasive ductal breast carcinoma juvenile dermatomyositis lung benign neoplasm ataxia-telangiectasia-like disorder 1 lymphoplasmacytic lymphoma benign colon neoplasm myopathy breast carcinoma cribriform carcinoma of breast oligodendroglioma
A [auth X], B [auth Y], C [auth Z]	Pharos: P39748	colorectal cancer malignant colon neoplasm metabolic syndrome X non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma rheumatoid arthritis aortic stenosis xeroderma pigmentosum group G breast cancer colorectal carcinoma ductal breast carcinoma in situ gallbladder disease large cell medulloblastoma lung cancer malignant mesothelioma colorectal cancer malignant colon neoplasm metabolic syndrome X non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma rheumatoid arthritis aortic stenosis xeroderma pigmentosum group G breast cancer colorectal carcinoma ductal breast carcinoma in situ gallbladder disease large cell medulloblastoma lung cancer malignant mesothelioma nasal cavity disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm subependymal giant cell astrocytoma asthma colorectal adenoma Colorectal Neoplasms endogenous depression inflammatory bowel disease laryngeal squamous cell carcinoma lymphoplasmacytic lymphoma medulloblastoma nasopharyngeal carcinoma ovarian cancer psoriasis ulcerative colitis bipolar I disorder Crohn disease endometriosis invasive ductal breast carcinoma lung adenocarcinoma

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.