4Q5V | pdb_00004q5v

Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and aphidicolin

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D [auth E]	Peptidase_M23	e4q5vE1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Peptidase_M23	ECOD (develop294)
A	DNA_pol_B	e4q5vA2	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: DNA_pol_B	ECOD (develop294)
A	DNA_pol_B_exo1	e4q5vA1	A: alpha bundles	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: DNA_pol_B_exo1	ECOD (develop294)
A	DNA_pol_B_exo1	e4q5vA6	A: alpha bundles	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: DNA_pol_B_exo1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth E]	2.40.50.730	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D [auth E]	3.30.70.2820	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D [auth E]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D [auth E]	1.10.132.60	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
A	2.40.50.730	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	3.30.70.2820	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.10.132.60	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth E]	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
A, D [auth E]	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F [auth G]	DNA template	-	-	-
B, E [auth F]	RNA primer	-	-	-
A, D [auth E]	DNA polymerase alpha catalytic subunit	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding 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 protein binding kinase binding enzyme binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding single-stranded DNA 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 DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation leading strand elongation nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA-templated DNA replication lagging strand elongation DNA strand elongation DNA strand elongation involved in DNA replication DNA replication initiation leading strand elongation regulation of biosynthetic process multicellular organismal process regulation of biological process regulation of cellular process type I interferon production biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process cytokine production regulation of cytokine production regulation of macromolecule biosynthetic process regulation of multicellular organismal process regulation of metabolic process regulation of type I interferon production DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair mitotic DNA replication cell cycle DNA replication initiation nuclear DNA replication cell cycle DNA replication mitotic DNA replication initiation mitotic cell cycle nuclear cell cycle DNA replication initiation mitotic cell cycle process cell cycle cell cycle process DNA synthesis involved in DNA repair DNA biosynthetic process double-strand break repair double-strand break repair via nonhomologous end joining	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix intracellular membraneless organelle nucleolus membraneless organelle organelle envelope nuclear envelope endomembrane system cytoplasm cytosol nucleoplasm chromatin chromosome protein-containing complex alpha DNA polymerase:primase complex nuclear protein-containing complex nuclear chromosome transferase complex nuclear replisome replication fork catalytic complex protein-DNA complex nuclear replication fork DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex replisome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth E]	IPR038256	DNA polymerase alpha, zinc finger domain superfamily	Homologous Superfamily
A, D [auth E]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, D [auth E]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A, D [auth E]	IPR045846	DNA polymerase alpha catalytic subunit, catalytic domain	Domain
A, D [auth E]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A, D [auth E]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, D [auth E]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
A, D [auth E]	IPR015088	Zinc finger, DNA-directed DNA polymerase, family B, alpha	Domain
A, D [auth E]	IPR006172	DNA-directed DNA polymerase, family B	Family
A, D [auth E]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, D [auth E]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A, D [auth E]	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A, D [auth E]	IPR024647	DNA polymerase alpha catalytic subunit, N-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D [auth E]	Pharos: P09884	X-linked reticulate pigmentary disorder ovarian cancer PIGMENTARY DISORDER, RETICULATE, WITH SYSTEMIC MANIFESTATIONS acute lymphoblastic leukemia atypical teratoid rhabdoid tumor intellectual disability malignant mesothelioma neurofibromatosis type 1 pancreatic adenocarcinoma primitive neuroectodermal tumor acute myeloid leukemia B-cell chronic lymphocytic leukemia large cell medulloblastoma malignant colon neoplasm mantle cell lymphoma X-linked reticulate pigmentary disorder ovarian cancer PIGMENTARY DISORDER, RETICULATE, WITH SYSTEMIC MANIFESTATIONS acute lymphoblastic leukemia atypical teratoid rhabdoid tumor intellectual disability malignant mesothelioma neurofibromatosis type 1 pancreatic adenocarcinoma primitive neuroectodermal tumor acute myeloid leukemia B-cell chronic lymphocytic leukemia large cell medulloblastoma malignant colon neoplasm mantle cell lymphoma non-small cell lung carcinoma tuberculosis acute promyelocytic leukemia glioblastoma malignant glioma medulloblastoma N syndrome

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.