3QE9 | pdb_00003qe9

Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with DNA (complex I)

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)
A [auth Y]		e3qe9Y1	A: POZ domain	X: POZ domain	H: POZ domain	T:	F:	ECOD (20:10:01)
D [auth Z]		e3qe9Z1	A: POZ domain	X: POZ domain	H: POZ domain	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth Y]	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
A [auth Y]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D [auth Z]	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
D [auth Z]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth Y], D [auth Z]	PF00867	XPG I-region (XPG_I)	XPG I-region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth Y], D [auth Z]	Exonuclease 1	single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease 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 catalytic activity exonuclease activity single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease 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 catalytic activity exonuclease activity 5'-flap endonuclease activity endonuclease activity DNA endonuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters chromatin binding binding DNA binding nucleic acid binding RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity RNA endonuclease activity double-stranded DNA 5'-3' DNA exonuclease activity double-stranded DNA exodeoxyribonuclease activity cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus mismatch repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair cellular response to stimulus mismatch repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair immune system development developmental process production of molecular mediator of immune response multicellular organismal process immunoglobulin production somatic diversification of immune receptors via somatic mutation gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins multicellular organism development biosynthetic process immune system process anatomical structure development somatic diversification of immune receptors somatic hypermutation of immunoglobulin genes system development formation of extrachromosomal circular DNA telomere organization chromosome organization cellular component biogenesis cellular component organization telomere maintenance organelle organization cellular component assembly telomere maintenance via telomere trimming t-circle formation cellular component organization or biogenesis DNA recombination DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication DNA strand resection involved in replication fork processing replication fork processing adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination B cell activation involved in immune response lymphocyte activation cell activation involved in immune response leukocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response leukocyte mediated immunity lymphocyte activation involved in immune response somatic recombination of immunoglobulin genes involved in immune response immune response B cell activation cell activation immunoglobulin mediated immune response adaptive immune response immune effector process somatic diversification of immune receptors via germline recombination within a single locus B cell mediated immunity isotype switching humoral immune response humoral immune response mediated by circulating immunoglobulin sexual reproduction reproductive process meiotic cell cycle cell cycle	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular membraneless organelle nuclear body membraneless organelle
C [auth D], F [auth B]	DNA (5'-D(PTPCPGPAPCPTPAPGPCPG)-3')	-	-	-
B [auth C], E [auth A]	DNA (5'-D(CPGPCPTPAPGPTPCPGPAPCPAP*T)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth Y], D [auth Z]	IPR044752	Exonuclease 1-like, PIN-like domain	Domain
A [auth Y], D [auth Z]	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A [auth Y], D [auth Z]	IPR019974	XPG conserved site	Conserved Site
A [auth Y], D [auth Z]	IPR037315	Exonuclease-1, H3TH domain	Domain
A [auth Y], D [auth Z]	IPR006084	XPG/Rad2 endonuclease	Family
A [auth Y], D [auth Z]	IPR006086	XPG-I domain	Domain
A [auth Y], D [auth Z]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A [auth Y], D [auth Z]	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A [auth Y], D [auth Z]	IPR006085	XPG, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth Y], D [auth Z]	Pharos: Q9UQ84	breast carcinoma colorectal cancer breast cancer Mammary Neoplasms non-small cell lung carcinoma peripheral nervous system disease psoriasis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ invasive ductal breast carcinoma lung cancer malignant mesothelioma osteosarcoma peripheral neuropathy skin basal cell carcinoma breast carcinoma colorectal cancer breast cancer Mammary Neoplasms non-small cell lung carcinoma peripheral nervous system disease psoriasis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ invasive ductal breast carcinoma lung cancer malignant mesothelioma osteosarcoma peripheral neuropathy skin basal cell carcinoma colorectal carcinoma glioblastoma large cell medulloblastoma malignant colon neoplasm medulloblastoma ovarian cancer primitive neuroectodermal tumor xeroderma pigmentosum group G hepatocellular carcinoma lung adenocarcinoma malignant glioma

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.