5EAY | pdb_00005eay

Crystal structure of a Dna2 peptide in complex with Rpa 70N

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)
D	SCOP2B Superfamily	Nucleic acid-binding proteins	8037540	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8037540	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8037540	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8037540	3000135	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)
D	Rep-A_N	e5eayD1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rep-A_N	ECOD (1.6)
C	Rep-A_N	e5eayC1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rep-A_N	ECOD (1.6)
B	Rep-A_N	e5eayB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rep-A_N	ECOD (1.6)
A	Rep-A_N	e5eayA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rep-A_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04057	Replication factor-A protein 1, N-terminal domain (Rep-A_N)	Replication factor-A protein 1, N-terminal domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	DNA replication ATP-dependent helicase/nuclease DNA2	nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity nuclease activity 5'-flap endonuclease activity endonuclease activity nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity nuclease activity 5'-flap endonuclease activity endonuclease activity hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters RNA binding binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding DNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides single-stranded DNA helicase activity cation binding metal ion 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 cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing cellular response to stress DNA damage response nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing cellular response to stress DNA damage response response to stress DNA repair cellular component organization organelle organization DNA geometric change chromosome organization DNA conformation change cellular component organization or biogenesis DNA replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity replication fork reversal replication fork processing 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 mitochondrial DNA metabolic process mitochondrial DNA replication formation of extrachromosomal circular DNA telomere organization cellular component biogenesis telomere maintenance cellular component assembly telomere maintenance via telomere trimming t-circle formation nuclear DNA replication cell cycle DNA replication telomere maintenance via semi-conservative replication cell cycle cell cycle process regulation of cell cycle phase transition signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cell communication negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction DNA replication checkpoint signaling regulation of cell cycle regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling lagging strand elongation DNA strand elongation DNA replication, Okazaki fragment processing DNA strand elongation involved in DNA replication base-excision repair mitochondrial DNA repair mitotic cell cycle mitotic telomere maintenance via semi-conservative replication mitotic cell cycle process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen intracellular membraneless organelle nucleoid mitochondrial matrix membraneless organelle mitochondrial nucleoid chromosome chromosome, telomeric region chromosomal region
A, B, C, D	Replication protein A 70 kDa DNA-binding subunit	chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding DNA binding damaged DNA binding nucleic acid binding sequence-specific DNA binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding telomeric DNA binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding DNA binding damaged DNA binding nucleic acid binding sequence-specific DNA binding G-rich strand telomeric DNA binding sequence-specific single stranded DNA binding single-stranded telomeric DNA binding single-stranded DNA binding telomeric DNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process localization cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process localization protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization telomere maintenance via telomerase telomere organization chromosome organization nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening telomere maintenance cellular component organization nucleic acid biosynthetic process organelle organization biosynthetic process cellular component organization or biogenesis DNA biosynthetic process multicellular organismal process multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells mismatch repair DNA repair DNA-templated DNA replication protein localization to site of double-strand break developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development DNA recombination multicellular organism development embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process double-strand break repair recombinational repair double-strand break repair via homologous recombination base-excision repair nucleotide-excision repair sexual reproduction reproductive process meiotic cell cycle cell cycle	membrane-bounded organelle protein-containing complex 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 membrane-bounded organelle protein-containing complex 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 DNA replication factor A complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome nucleoplasm condensed nuclear chromosome lateral element synaptonemal structure synaptonemal complex condensed chromosome male germ cell nucleus germ cell nucleus site of double-strand break site of DNA damage chromosome, telomeric region chromosomal region nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR041677	DNA2/NAM7 helicase, helicase domain	Domain
E, F, G, H	IPR026851	DNA replication ATP-dependent helicase/nuclease Dna2/JHS1, DEXXQ-box helicase domain	Domain
E, F, G, H	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
E, F, G, H	IPR048459	DNA2, rift barrel domain	Domain
E, F, G, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E, F, G, H	IPR014808	DNA replication factor Dna2, N-terminal	Domain
E, F, G, H	IPR051827	CRISPR-associated exonuclease Cas4	Family
E, F, G, H	IPR011604	PD-(D/E)XK endonuclease-like domain superfamily	Homologous Superfamily
E, F, G, H	IPR047187	Upf1-like, C-terminal helicase domain	Domain
A, B, C, D	IPR007199	Replication factor-A protein 1, N-terminal	Domain
A, B, C, D	IPR047192	Replication factor A, C-terminal, eukaryotes	Domain
A, B, C, D	IPR013955	Replication factor A, C-terminal	Domain
A, B, C, D	IPR031657	Replication protein A, OB domain	Domain
A, B, C, D	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type	Domain
A, B, C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C, D	IPR004591	Replication factor A protein 1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: P51530	mitochondrial DNA deletion syndrome with progressive myopathy progressive external ophthalmoplegia Seckel syndrome 8 intellectual disability breast cancer isolated growth hormone deficiency type IA malignant colon neoplasm microcephaly muscle tissue disease nasopharyngeal carcinoma Primary microcephaly psoriasis cerebrovascular disorder large cell medulloblastoma malignant mesothelioma mitochondrial DNA deletion syndrome with progressive myopathy progressive external ophthalmoplegia Seckel syndrome 8 intellectual disability breast cancer isolated growth hormone deficiency type IA malignant colon neoplasm microcephaly muscle tissue disease nasopharyngeal carcinoma Primary microcephaly psoriasis cerebrovascular disorder large cell medulloblastoma malignant mesothelioma muscular disease non-small cell lung carcinoma primitive neuroectodermal tumor lung cancer medulloblastoma myopathy ovarian cancer
A, B, C, D	Pharos: P27694	Chloracne astrocytic tumor breast cancer glioblastoma malignant ependymoma ovarian cancer atypical teratoid rhabdoid tumor Hodgkins lymphoma malignant mesothelioma psoriasis B-cell chronic lymphocytic leukemia dermatomyositis lymphoplasmacytic lymphoma medulloblastoma

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.