1EFY

CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF POLY (ADP-RIBOSE) POLYMERASE COMPLEXED WITH A BENZIMIDAZOLE INHIBITOR

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1efya1	All alpha proteins	Domain of poly(ADP-ribose) polymerase	Domain of poly(ADP-ribose) polymerase	Domain of poly(ADP-ribose) polymerase	Domain of poly(ADP-ribose) polymerase	chicken (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
A	d1efya2	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	Poly(ADP-ribose) polymerase, C-terminal domain	Poly(ADP-ribose) polymerase, C-terminal domain	chicken (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Poly(ADP-ribose) polymerase, C-terminal domain	8024639	4002425	SCOP2 (2022-06-29)
A	SCOP2 Family	Domain of poly(ADP-ribose) polymerase	8025033	4000968	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ADP-ribosylation	8037018	3001208	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Domain of poly(ADP-ribose) polymerase	8037412	3000280	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PARP_reg	e1efyA1	A: alpha bundles	X: Domain of poly(ADP-ribose) polymerase (From Topology)	H: Domain of poly(ADP-ribose) polymerase (From Topology)	T: Domain of poly(ADP-ribose) polymerase	F: PARP_reg	ECOD (1.6)
A	PARP	e1efyA2	A: a+b complex topology	X: ADP-ribosylation (From Topology)	H: ADP-ribosylation (From Topology)	T: ADP-ribosylation	F: PARP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.142.10	Mainly Alpha	Up-down Bundle	Poly(ADP-ribose) Polymerase	domain 1	CATH (4.3.0)
A	3.90.228.10	Alpha Beta	Alpha-Beta Complex	Phosphoenolpyruvate Carboxykinase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00644	Poly(ADP-ribose) polymerase catalytic domain (PARP)	Poly(ADP-ribose) polymerase catalytic domain	-	Family
A	PF02877	Poly(ADP-ribose) polymerase, regulatory domain (PARP_reg)	Poly(ADP-ribose) polymerase, regulatory domain	Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component ...	Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	POLY (ADP-RIBOSE) POLYMERASE	pentosyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity NAD+-protein ADP-ribosyltransferase activity transferase activity catalytic activity NAD+-protein poly-ADP-ribosyltransferase activity DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding NAD+-protein-tyrosine ADP-ribosyltransferase activity identical protein binding pentosyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity NAD+-protein ADP-ribosyltransferase activity transferase activity catalytic activity NAD+-protein poly-ADP-ribosyltransferase activity DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding NAD+-protein-tyrosine ADP-ribosyltransferase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity NAD+-protein-aspartate ADP-ribosyltransferase activity NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups NAD+-protein-glutamate ADP-ribosyltransferase activity NAD+-protein-histidine ADP-ribosyltransferase activity protein-containing complex binding chromatin binding nucleosome binding NAD+-protein-serine ADP-ribosyltransferase activity	nucleobase-containing compound metabolic process DNA modification macromolecule modification metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA ADP-ribosylation regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms negative regulation of response to biotic stimulus nucleobase-containing compound metabolic process DNA modification macromolecule modification metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA ADP-ribosylation regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms negative regulation of response to biotic stimulus response to stimulus regulation of response to external stimulus negative regulation of biological process response to biotic stimulus response to stress regulation of response to stress innate immune response regulation of immune system process response to external biotic stimulus regulation of biological process negative regulation of response to stimulus immune response response to other organism defense response regulation of innate immune response negative regulation of immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus negative regulation of immune system process immune system process defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response negative regulation of innate immune response DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity replication fork reversal DNA replication replication fork processing ribose phosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process ATP generation from poly-ADP-D-ribose purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process purine nucleoside triphosphate metabolic process nucleotide metabolic process purine-containing compound metabolic process organophosphate metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair cellular response to stress recombinational repair positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination positive regulation of cellular process DNA repair positive regulation of DNA recombination double-strand break repair positive regulation of nucleobase-containing compound metabolic process DNA recombination regulation of macromolecule metabolic process positive regulation of double-strand break repair regulation of DNA repair regulation of double-strand break repair via homologous recombination positive regulation of DNA metabolic process DNA damage response regulation of metabolic process regulation of DNA metabolic process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process protein poly-ADP-ribosylation protein metabolic process post-translational protein modification protein modification process protein auto-ADP-ribosylation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol chromatin chromosome nuclear replication fork nuclear chromosome replication fork site of double-strand break site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR049296	PARP1-like, PADR1 domain, N-terminal helical subdomain	Domain
A	IPR038650	PADR1, C-terminal domain superfamily	Homologous Superfamily
A	IPR012317	Poly(ADP-ribose) polymerase, catalytic domain	Domain
A	IPR036957	Zinc finger, PARP-type superfamily	Homologous Superfamily
A	IPR001357	BRCT domain	Domain
A	IPR050800	ADP-ribosyltransferase diphtheria toxin-like	Family
A	IPR036420	BRCT domain superfamily	Homologous Superfamily
A	IPR036616	Poly(ADP-ribose) polymerase, regulatory domain superfamily	Homologous Superfamily
A	IPR036930	WGR domain superfamily	Homologous Superfamily
A	IPR001510	Zinc finger, PARP-type	Domain
A	IPR004102	Poly(ADP-ribose) polymerase, regulatory domain	Domain
A	IPR008288	Poly [ADP-ribose] polymerase	Family
A	IPR008893	WGR domain	Domain
A	IPR012982	PARP1-like, PADR1 domain, zinc ribbon fold	Domain

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.