3P87 | pdb_00003p87

Structure of human PCNA bound to RNASEH2B PIP box peptide

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)
K [auth F]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
K [auth F]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	DNA clamp	8032796	3000780	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8032799	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8032796	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)
K [auth F]	AAA	e3p87F1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
I [auth E]	AAA	e3p87E1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
G [auth D]	AAA	e3p87D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
E [auth C]	AAA	e3p87C1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
C [auth B]	AAA	e3p87B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
A	PCNA_C	e3p87A1	A: alpha bundles	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: Macro domain-like	T: Macro domain-like	F: PCNA_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K [auth F]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
I [auth E]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
G [auth D]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
E [auth C]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
C [auth B]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
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
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	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, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	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
B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	Ribonuclease H2 subunit B	-	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process biosynthetic process gene expression catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process biosynthetic process gene expression macromolecule biosynthetic process fibroblast proliferation cell population proliferation cellular response to stimulus mismatch repair response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair cell cycle G2/M phase transition regulation of biological process regulation of cell cycle phase transition regulation of cellular process regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process G2/M transition of mitotic cell cycle biological regulation regulation of cell cycle G2/M phase transition cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle cell cycle process mitotic cell cycle phase transition ribose phosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative metabolic process nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process positive regulation of cell population proliferation positive regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation positive regulation of cellular process regulation of biosynthetic process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of macromolecule metabolic process DNA damage checkpoint signaling signaling regulation of cellular response to stress negative regulation of cell cycle regulation of signal transduction intracellular signal transduction cell communication regulation of cell cycle checkpoint regulation of intracellular signal transduction regulation of response to stress negative regulation of cell cycle phase transition signal transduction regulation of signaling DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of response to stimulus signal transduction in response to DNA damage regulation of cell communication regulation of DNA damage checkpoint developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development	protein-containing complex catalytic complex intracellular protein-containing complex ribonuclease H2 complex 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 protein-containing complex catalytic complex intracellular protein-containing complex ribonuclease H2 complex 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
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	IPR040456	Ribonuclease H2 subunit B	Family
B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	IPR041195	Rnh202, triple barrel domain	Domain
B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	IPR019024	Ribonuclease H2 subunit B, wHTH domain	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR046938	DNA clamp superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	Pharos: Q5TBB1	Aicardi-Goutieres syndrome Aicardi-Goutieres syndrome 2 astrocytic tumor Epileptic encephalopathy malignant mesothelioma pseudo-TORCH syndrome Aicardi-Goutieres syndrome 1 benign prostatic hyperplasia intellectual disability medulloblastoma tuberculosis leukodystrophy osteosarcoma
A, C [auth B], E [auth C], G [auth D], I [auth E], A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	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

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.