5YD8

Crystal structure of human PCNA in complex with APIM of human ZRANB3

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth Y]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
A [auth Y]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
B [auth X]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
B [auth X]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C [auth Z]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C [auth Z]	SCOP2B Superfamily	DNA clamp	8032799	3000780	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 Y]	PCNA_N	e5yd8Y2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N	ECOD (1.6)
A [auth Y]	PCNA_C	e5yd8Y1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
B [auth X]	PCNA_N	e5yd8X1	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 X]	PCNA_C	e5yd8X2	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 Z]	PCNA_N	e5yd8Z2	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 Z]	PCNA_C	e5yd8Z1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth Y]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
B [auth X]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
C [auth Z]	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
A [auth Y], B [auth X], C [auth Z]	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
A [auth Y], B [auth X], C [auth Z]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth Y], B [auth X], C [auth Z]	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 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 positive regulation of nucleobase-containing compound metabolic 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 postreplication repair nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process 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 organic cyclic compound 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 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 positive regulation of biosynthetic process positive regulation of transferase activity positive regulation of DNA biosynthetic process regulation of DNA-directed DNA polymerase activity regulation of DNA-templated DNA replication positive regulation of DNA-directed DNA polymerase activity 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 nuclear periphery nuclear lamina nuclear body protein-DNA complex replisome
D [auth W], E [auth U], F [auth V]	ZRANB3	catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds hydrolase activity DNA nuclease activity polyubiquitin modification-dependent protein binding protein binding binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds hydrolase activity DNA nuclease activity polyubiquitin modification-dependent protein binding protein binding binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity 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 ATP-dependent DNA/DNA annealing activity DNA binding DNA/DNA annealing activity annealing activity single-stranded DNA binding nucleic acid binding cation binding transition metal ion binding zinc ion binding metal ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process 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 response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process 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 macromolecule metabolic process replication fork processing replication fork reversal regulation of DNA recombination regulation of cellular process negative regulation of biological process regulation of primary metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of metabolic process DNA recombination biological regulation regulation of macromolecule metabolic process negative regulation of DNA recombination negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process response to light stimulus response to radiation response to abiotic stimulus response to UV DNA repair cellular component organization organelle organization DNA rewinding DNA geometric change chromosome organization DNA conformation change cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen nuclear replication fork intracellular membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen nuclear replication fork intracellular membraneless organelle nuclear chromosome chromosome membraneless organelle replication fork

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth Y], B [auth X], C [auth Z]	IPR046938	DNA clamp superfamily	Homologous Superfamily
A [auth Y], B [auth X], C [auth Z]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
A [auth Y], B [auth X], C [auth Z]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
A [auth Y], B [auth X], C [auth Z]	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
A [auth Y], B [auth X], C [auth Z]	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
D [auth W], E [auth U], F [auth V]	IPR000330	SNF2, N-terminal	Domain
D [auth W], E [auth U], F [auth V]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
D [auth W], E [auth U], F [auth V]	IPR003615	HNH nuclease	Domain
D [auth W], E [auth U], F [auth V]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
D [auth W], E [auth U], F [auth V]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D [auth W], E [auth U], F [auth V]	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
D [auth W], E [auth U], F [auth V]	IPR001650	Helicase, C-terminal domain-like	Domain
D [auth W], E [auth U], F [auth V]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
D [auth W], E [auth U], F [auth V]	IPR001876	Zinc finger, RanBP2-type	Domain
D [auth W], E [auth U], F [auth V]	IPR002711	HNH endonuclease	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth Y], B [auth X], C [auth Z]	Pharos: P12004	psoriasis ataxia-telangiectasia-like disorder 2 hepatoblastoma adenocarcinoma malignant colon neoplasm granular cell carcinoma Radiation Injuries, Experimental tubular adenocarcinoma focal segmental glomerulosclerosis pancreatic intraductal papillary-mucinous neoplasm endometriosis primitive neuroectodermal tumor glioblastoma 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 pancreatic intraductal papillary-mucinous neoplasm endometriosis primitive neuroectodermal tumor glioblastoma pustulosis palmaris et plantaris Sjogren syndrome large cell medulloblastoma lung cancer astrocytic tumor nasopharyngeal carcinoma neurodegenerative disease colonic neoplasm ovarian cancer dermatomyositis pituitary cancer IgA glomerulonephritis ischemic disease lung adenocarcinoma ataxia-telangiectasia-like disorder malignant glioma atypical teratoid rhabdoid tumor medulloblastoma brain cancer breast cancer non-small cell lung carcinoma cribriform carcinoma pancreatic intraductal papillary-mucinous carcinoma ductal breast carcinoma in situ invasive ductal breast carcinoma juvenile dermatomyositis lung benign neoplasm lymphoplasmacytic lymphoma ataxia-telangiectasia-like disorder 1 benign colon neoplasm myopathy breast carcinoma oligodendroglioma cribriform carcinoma of breast
D [auth W], E [auth U], F [auth V]	Pharos: Q5FWF4	astrocytic tumor osteosarcoma cardiac arrest colorectal cancer

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.