5VBN | pdb_00005vbn

Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNA_pol_E_B	e5vbnA2	A: a/b three-layered sandwiches	X: RING/U-box-like	H: UDP-Glycosyltransferase/glycogen phosphorylase	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: DNA_pol_E_B	ECOD (v294.1)
C [auth E]	Acetone_carb_G	e5vbnE1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: Acetone_carb_G	ECOD (v294.1)
B	zf_DPOE_2	e5vbnB1	A: a/b three-layered sandwiches	X: RING/U-box-like	H: UDP-Glycosyltransferase/glycogen phosphorylase	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: zf_DPOE_2	ECOD (v294.1)
B	DNA_alkylation	e5vbnB2	A: a/b three-layered sandwiches	X: RING/U-box-like	H: UDP-Glycosyltransferase/glycogen phosphorylase	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: DNA_alkylation	ECOD (v294.1)
D [auth F]	Acetone_carb_G	e5vbnF1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: Acetone_carb_G	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth E]	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family
B, D [auth F]	PF22912	Zinc finger domain of DNA polymerase-epsilon (zf-DPOE)	Zinc finger domain of DNA polymerase-epsilon	This zinc finger domain is found in the epsilon subunit of DNA polymerase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth E]	DNA polymerase epsilon subunit 2	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 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 translesion synthesis cellular response to stimulus response to stimulus nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic 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 translesion synthesis cellular response to stimulus response to stimulus nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process cellular response to stress DNA damage response response to stress error-prone translesion synthesis DNA biosynthetic process DNA repair DNA-templated 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 membraneless organelle catalytic complex 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 membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle epsilon DNA polymerase complex DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular protein-containing complex nuclear lumen nuclear body nucleoplasm
B, D [auth F]	DNA polymerase epsilon catalytic subunit A	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule 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 single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule 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 single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity catalytic activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity chromatin binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	cellular process cell cycle mitotic cell cycle nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication leading strand elongation DNA strand elongation DNA strand elongation involved in DNA replication cellular process cell cycle mitotic cell cycle nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication leading strand elongation DNA strand elongation DNA strand elongation involved in DNA replication cellular response to stimulus response to stimulus DNA-templated DNA replication maintenance of fidelity DNA replication proofreading cellular response to stress DNA damage response response to stress DNA repair developmental process multicellular organism development multicellular organismal process anatomical structure development animal organ development embryonic organ development embryo development mitotic cell cycle process cell cycle phase transition G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle phase transition cell cycle process nucleotide-excision repair, DNA gap filling nucleotide-excision repair base-excision repair, gap-filling base-excision repair nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process	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 membraneless organelle catalytic complex 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 membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle epsilon DNA polymerase complex DNA polymerase complex transferase complex, transferring phosphorus-containing groups organelle lumen organelle intracellular protein-containing complex nuclear lumen cell periphery plasma membrane membrane nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth E]	IPR016266	DNA polymerase epsilon, subunit B	Family
A, C [auth E]	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
A, C [auth E]	IPR024639	DNA polymerase epsilon subunit B, N-terminal	Domain
B, D [auth F]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B, D [auth F]	IPR054475	DNA polymerase-epsilon, zinc finger domain	Domain
B, D [auth F]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B, D [auth F]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
B, D [auth F]	IPR006172	DNA-directed DNA polymerase, family B	Family
B, D [auth F]	IPR029703	DNA polymerase epsilon catalytic subunit	Family
B, D [auth F]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B, D [auth F]	IPR013697	DNA polymerase epsilon, catalytic subunit A, C-terminal	Domain
B, D [auth F]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
B, D [auth F]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
B, D [auth F]	IPR055191	DNA polymerase epsilon ,catalytic subunit A, thumb domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth E]	Pharos: P56282	acute myeloid leukemia breast cancer invasive ductal breast carcinoma malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor adrenal cortex carcinoma ductal breast carcinoma in situ large cell medulloblastoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis atypical teratoid rhabdoid tumor acute myeloid leukemia breast cancer invasive ductal breast carcinoma malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor adrenal cortex carcinoma ductal breast carcinoma in situ large cell medulloblastoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm psoriasis atypical teratoid rhabdoid tumor glioblastoma lung cancer medulloblastoma ovarian cancer pilocytic astrocytoma
B, D [auth F]	Pharos: Q07864	facial dysmorphism-immunodeficiency-livedo-short stature syndrome colorectal cancer, susceptibility to, 12 colorectal cancer malignant mesothelioma medulloblastoma mismatch repair cancer syndrome osteosarcoma acute lymphoblastic leukemia prostate carcinoma atrial fibrillation skin neoplasm colorectal adenocarcinoma colorectal carcinoma endometriosis gastric carcinoma facial dysmorphism-immunodeficiency-livedo-short stature syndrome colorectal cancer, susceptibility to, 12 colorectal cancer malignant mesothelioma medulloblastoma mismatch repair cancer syndrome osteosarcoma acute lymphoblastic leukemia prostate carcinoma atrial fibrillation skin neoplasm colorectal adenocarcinoma colorectal carcinoma endometriosis gastric carcinoma Lymphomatous meningitis ovarian cancer acute myeloid leukemia psoriasis benign colon neoplasm stomach carcinoma in situ endometrium carcinoma in situ gastric neoplasm Lynch syndrome non-small cell lung carcinoma pancreatic adenocarcinoma acute promyelocytic leukemia skin cancer benign neoplasm of stomach uterine disease endometrial carcinoma

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.