1NH3 | pdb_00001nh3

Human Topoisomerase I Ara-C Complex

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
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth A]	d1nh3a1	Alpha and beta proteins (a+b)	DNA breaking-rejoining enzymes	DNA breaking-rejoining enzymes	Eukaryotic DNA topoisomerase I, catalytic core	Eukaryotic DNA topoisomerase I, catalytic core	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d1nh3a2	Multi-domain proteins (alpha and beta)	Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8042712	3001127	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8042712	3001127	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Eukaryotic DNA topoisomerase I N-terminal DNA-binding domain-like	8042713	3001820	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 [auth A]		e1nh3A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: PABC(PABP) domain	H: PABC(PABP) domain	T: PABP	F:	ECOD (20:10:01)
D [auth A]		e1nh3A2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Topoisom_I,Topo_C_assoc	F:	ECOD (20:10:01)
D [auth A]		e1nh3A4	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: IMS_HHH	F:	ECOD (20:10:01)
D [auth A]		e1nh3A5	A: Lipocalins/Streptavidin	X: SAM/DNA-glycosylase	H: SAM domain-like	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	1.10.10.41	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Yeast DNA topoisomerase - domain 1	CATH (4.3.0)
D [auth A]	2.170.11.10	Mainly Beta	Beta Complex	DNA Topoisomerase I	domain 2	CATH (4.3.0)
D [auth A]	3.90.15.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase I	Chain A, domain 3	CATH (4.3.0)
D [auth A]	1.10.132.10	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
D [auth A]	PF02919	Eukaryotic DNA topoisomerase I, DNA binding fragment (Topoisom_I_N)	Eukaryotic DNA topoisomerase I, DNA binding fragment	-	Family
D [auth A]	PF01028	Eukaryotic DNA topoisomerase I, catalytic core (Topoisom_I)	Eukaryotic DNA topoisomerase I, catalytic core	Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth A]	DNA topoisomerase I	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 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 small molecule binding DNA binding nucleic acid binding double-stranded DNA binding supercoiled DNA binding protein-containing complex binding protein binding protein domain specific binding sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups chromatin DNA binding nucleic acid conformation isomerase activity isomerase activity DNA topoisomerase type I (single strand cut, ATP-independent) activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity, acting on a nucleic acid macromolecular conformation isomerase activity DNA binding, bending single-stranded DNA binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cellular process cell division embryo development cell cycle chromosome segregation cell cycle process response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cellular process cell division embryo development cell cycle chromosome segregation cell cycle process cell death programmed cell death chromosome organization primary metabolic process DNA conformation change DNA metabolic process nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process DNA topological change organelle organization metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of biosynthetic process rhythmic process regulation of biological process regulation of cellular process circadian regulation of gene expression circadian rhythm biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process response to abiotic stimulus response to temperature stimulus RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process rRNA transcription rRNA metabolic process response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to stimulus cellular response to nitrogen compound cellular response to gonadotropin stimulus cellular response to luteinizing hormone stimulus response to endogenous stimulus response to luteinizing hormone response to peptide hormone cellular response to peptide hormone stimulus cellular response to oxygen-containing compound response to gonadotropin cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone cellular response to hormone stimulus DNA replication response to ionizing radiation response to radiation response to gamma radiation animal organ regeneration animal organ development regeneration chromatin organization chromatin remodeling	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular organelle intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome membrane-bounded organelle male germ cell nucleus nucleus somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular organelle intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome membrane-bounded organelle male germ cell nucleus nucleus germ cell nucleus intracellular membrane-bounded organelle membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm dense fibrillar component fibrillar center protein-containing complex protein-DNA complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule cytoplasm supramolecular complex P-body
C [auth D]	5'-D(APAPAPAPAPTPUPUPUPUPCP(CAR)PAPAPGPUPCPUPUPUPUPT)-3'	-	-	-
B [auth C]	5'-D((GNG)PGPAPAPAPAPAPUPUPUPUPT)-3'	-	-	-
A [auth B]	5'-D(APAPAPAPAPGPAPCPUP(UBB))-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A]	IPR048045	DNA topoisomerase I, DNA-binding domain	Domain
D [auth A]	IPR011010	DNA breaking-rejoining enzyme, catalytic core	Homologous Superfamily
D [auth A]	IPR001631	DNA topoisomerase I	Family
D [auth A]	IPR018521	DNA topoisomerase IB, active site	Active Site
D [auth A]	IPR036202	DNA topoisomerase I, DNA binding, eukaryotic-type, N-terminal domain superfamily	Homologous Superfamily
D [auth A]	IPR013030	DNA topoisomerase I, DNA binding, N-terminal domain 2	Homologous Superfamily
D [auth A]	IPR025834	Topoisomerase I C-terminal domain	Domain
D [auth A]	IPR014727	DNA topoisomerase I, catalytic core, alpha/beta subdomain	Homologous Superfamily
D [auth A]	IPR013499	DNA topoisomerase I, eukaryotic-type	Domain
D [auth A]	IPR051062	DNA topoisomerase IB	Family
D [auth A]	IPR008336	DNA topoisomerase I, DNA binding, eukaryotic-type	Domain
D [auth A]	IPR014711	DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type	Homologous Superfamily
D [auth A]	IPR013500	DNA topoisomerase I, catalytic core, eukaryotic-type	Domain
D [auth A]	IPR013034	DNA topoisomerase I, DNA binding, N-terminal domain 1	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth A]	Pharos: P11387	cancer systemic sclerosis acute myeloid leukemia benign neoplasm Drug-Related Side Effects and Adverse Reactions malignant colon neoplasm non-small cell lung carcinoma psoriasis heart disease myopathy ovarian cancer astrocytic tumor juvenile dermatomyositis pancreatic adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth A]	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048
C [auth D]	CAR	Parent Component: DC RESID: AA0039
B [auth C]	GNG	Parent Component: G RESID: AA0039
A [auth B]	UBB	Parent Component: U RESID: AA0039

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.