Annotations: 9EKB

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Metallo-dependent phosphatases	8053383	3001067	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8053386	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8054002	3000034	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14260	C4-type zinc-finger of DNA polymerase delta (zf-C4pol)	C4-type zinc-finger of DNA polymerase delta	In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1 [1]. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and thr ...	In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1 [1]. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1 [2].	Domain
A	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
B	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
B	PF18018	DNA polymerase delta subunit OB-fold domain (DNA_pol_D_N)	DNA polymerase delta subunit OB-fold domain	The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance [1]. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond ...	The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance [1]. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond to the three subunits of S. cerevisiae Pol delta. p50 serves as a scaffold for the assembly of Pol delta by interacting simultaneously with all of the other three subunits. This entry corresponds to the OB fold domain found in the p50 subunit.	Domain
C	PF09507	DNA polymerase subunit Cdc27 (CDC27)	DNA polymerase subunit Cdc27	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA polymerase delta catalytic subunit	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding DNA binding damaged DNA binding nucleic acid binding DNA exonuclease activity catalytic activity, acting on a nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding DNA binding damaged DNA binding nucleic acid binding DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding ion binding metal ion binding protein binding enzyme binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process translesion synthesis cellular response to stimulus postreplication repair response to stimulus nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process translesion synthesis cellular response to stimulus postreplication repair response to stimulus nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process error-free translesion synthesis nucleic acid biosynthetic process cellular response to stress biosynthetic process DNA damage response response to stress DNA biosynthetic process DNA repair DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication proofreading fatty acid homeostasis chemical homeostasis homeostatic process lipid homeostasis response to light stimulus response to radiation response to abiotic stimulus response to UV cellular response to radiation cellular response to environmental stimulus cellular response to light stimulus cellular response to abiotic stimulus cellular response to UV nucleotide-excision repair, DNA gap filling nucleotide-excision repair base-excision repair, gap-filling base-excision repair	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle nuclear replisome membraneless organelle replication fork delta DNA polymerase complex catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular protein-containing complex nuclear lumen replisome inclusion body aggresome nucleoplasm nucleotide-excision repair complex
B	DNA polymerase delta subunit 2	DNA binding binding nucleic acid binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process DNA-templated DNA replication nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process DNA-templated DNA replication DNA strand elongation DNA strand elongation involved in DNA replication translesion synthesis cellular response to stimulus postreplication repair response to stimulus DNA synthesis involved in DNA repair cellular response to stress DNA damage response response to stress error-prone translesion synthesis DNA repair	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork delta DNA polymerase complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome nucleoplasm
C	DNA polymerase delta subunit 3	protein-macromolecule adaptor activity molecular adaptor activity	primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA strand elongation primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA strand elongation DNA replication DNA strand elongation involved in DNA replication translesion synthesis cellular response to stimulus postreplication repair response to stimulus DNA synthesis involved in DNA repair cellular response to stress DNA damage response response to stress error-prone translesion synthesis DNA repair mismatch repair nucleotide-excision repair, DNA gap filling nucleotide-excision repair response to light stimulus cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation response to UV UV-damage excision repair response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV DNA synthesis involved in UV-damage excision repair	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork delta DNA polymerase complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome cytoplasm nucleoplasm
D	DNA polymerase delta subunit 4	-	regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation biological regulation positive regulation of biological process regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation cellular process regulation of epithelial cell proliferation epithelial cell proliferation regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation biological regulation positive regulation of biological process regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation cellular process regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of cellular process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process cellular response to stress biosynthetic process DNA damage response response to stress metabolic process macromolecule metabolic process DNA biosynthetic process DNA repair DNA-templated DNA replication DNA replication	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork delta DNA polymerase complex catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular protein-containing complex nuclear lumen replisome nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A	IPR050240	DNA polymerase type-B	Family
A	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR025687	C4-type zinc-finger of DNA polymerase delta	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR056435	DNA polymerase delta/zeta catalytic subunit, N-terminal domain	Domain
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
B	IPR024826	DNA polymerase delta/II small subunit family	Family
B	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
B	IPR040663	DNA polymerase delta subunit, OB-fold domain	Domain
B	IPR041863	DNA polymerase delta subunit 2, C-terminal domain	Domain
C	IPR019038	DNA polymerase delta subunit 3	Family
C	IPR041913	DNA polymerase delta subunit 3 superfamily	Homologous Superfamily
D	IPR007218	DNA polymerase delta, subunit 4	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P28340	mandibular hypoplasia-deafness-progeroid syndrome lipodystrophy colorectal cancer, susceptibility to, 10 hypogonadism Jaw Abnormalities colorectal cancer endometrial carcinoma lung adenocarcinoma acute promyelocytic leukemia ovarian cancer primary biliary cholangitis colorectal carcinoma psoriasis endometrial cancer large cell medulloblastoma mandibular hypoplasia-deafness-progeroid syndrome lipodystrophy colorectal cancer, susceptibility to, 10 hypogonadism Jaw Abnormalities colorectal cancer endometrial carcinoma lung adenocarcinoma acute promyelocytic leukemia ovarian cancer primary biliary cholangitis colorectal carcinoma psoriasis endometrial cancer large cell medulloblastoma medulloblastoma acute lymphoblastic leukemia atypical teratoid rhabdoid tumor pancreatic adenocarcinoma hypogonadotropic hypogonadism malignant mesothelioma acute myeloid leukemia non-small cell lung carcinoma benign colon neoplasm primitive neuroectodermal tumor
B	Pharos: P49005	carpal tunnel syndrome metabolic syndrome X Sjogren syndrome lung cancer oligodendroglioma malignant ependymoma ovarian cancer
C	Pharos: Q15054	colorectal cancer colorectal adenoma Colorectal Neoplasms malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma medulloblastoma colorectal carcinoma malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm

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.