8B8T

Open conformation of the complex of DNA ligase I on PCNA and DNA in the presence of ATP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth E]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ATP-dependent DNA ligase DNA-binding domain	8043718	3001985	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 E]	PCNA_N	e8b8tE1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N	ECOD (1.6)
B [auth E]	PCNA_C	e8b8tE2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
C [auth F]	PCNA_N	e8b8tF2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N	ECOD (1.6)
C [auth F]	PCNA_C	e8b8tF1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
D [auth G]	PCNA_N	e8b8tG2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N	ECOD (1.6)
D [auth G]	PCNA_C	e8b8tG1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
A	DNA_ligase_A_N	e8b8tA2	A: alpha bundles	X: ATP-dependent DNA ligase DNA-binding domain (From Topology)	H: ATP-dependent DNA ligase DNA-binding domain (From Topology)	T: ATP-dependent DNA ligase DNA-binding domain	F: DNA_ligase_A_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E], C [auth F], D [auth G]	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
B [auth E], C [auth F], D [auth G]	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	PF04675	DNA ligase N terminus (DNA_ligase_A_N)	DNA ligase N terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth E], C [auth F], D [auth G]	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 organic cyclic compound 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 nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA-templated DNA replication maintenance of fidelity metabolic process primary metabolic process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA-templated DNA replication maintenance of fidelity metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process replication fork processing nucleic acid metabolic process 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 cellular process DNA repair positive regulation of nucleobase-containing compound metabolic process regulation of biological process positive regulation of DNA replication biological regulation positive regulation of biological process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of DNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound 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 postreplication repair cellular biosynthetic process DNA synthesis involved in DNA repair nucleic acid biosynthetic process translesion synthesis cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process biosynthetic process DNA biosynthetic process regulation of cellular process regulation of cellular response to stress positive regulation of response to stimulus positive regulation of DNA repair regulation of response to stress positive regulation of cellular process 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 organic cyclic compound response to acid chemical response to organonitrogen compound 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 cellular 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 regulation of cellular metabolic process gene expression negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process 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 regulation of catalytic activity positive regulation of molecular function regulation of deoxyribonuclease activity regulation of nuclease activity positive regulation of deoxyribonuclease activity positive regulation of nuclease activity positive regulation of catalytic activity regulation of molecular function positive regulation of hydrolase activity regulation of hydrolase activity regulation of transferase activity regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process regulation of DNA-directed DNA polymerase activity positive regulation of DNA-directed DNA polymerase activity positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of transferase activity positive regulation of DNA biosynthetic process regulation of DNA-templated DNA replication positive regulation of cellular biosynthetic process 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 extracellular organelle extracellular region organelle extracellular space 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 extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle 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 nuclear periphery nuclear lamina nuclear body replisome
A	DNA ligase 1	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 organic cyclic compound 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 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 DNA strand elongation involved in DNA replication macromolecule metabolic process cellular process cell division cellular response to stimulus 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 DNA strand elongation involved in DNA replication macromolecule metabolic process cellular process cell division cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair mitotic DNA replication nuclear DNA replication cell cycle DNA replication Okazaki fragment processing involved in mitotic DNA replication mitotic cell cycle mitotic cell cycle process DNA replication, Okazaki fragment processing cell cycle cell cycle process developmental process anatomical structure morphogenesis anatomical structure development DNA recombination cellular biosynthetic process cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process base-excision repair base-excision repair, gap-filling DNA ligation	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth E], C [auth F], D [auth G]	IPR046938	DNA clamp superfamily	Homologous Superfamily
B [auth E], C [auth F], D [auth G]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
B [auth E], C [auth F], D [auth G]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
B [auth E], C [auth F], D [auth G]	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
B [auth E], C [auth F], D [auth G]	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
A	IPR036599	DNA ligase, ATP-dependent, N-terminal domain superfamily	Homologous Superfamily
A	IPR012310	DNA ligase, ATP-dependent, central	Domain
A	IPR012308	DNA ligase, ATP-dependent, N-terminal	Domain
A	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
A	IPR000977	DNA ligase, ATP-dependent	Family
A	IPR050191	ATP-dependent DNA ligase	Family
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR012309	DNA ligase, ATP-dependent, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth E], C [auth F], D [auth G]	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 lung cancer astrocytic tumor 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	Pharos: P18858	urinary bladder cancer adrenal cortex carcinoma medulloblastoma colorectal cancer osteosarcoma urinary bladder neoplasm malignant mesothelioma primitive neuroectodermal tumor xeroderma pigmentosum group G

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.