Annotations: 1K4S

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth A]	d1k4sa1	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]	d1k4sa2	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	Eukaryotic DNA topoisomerase I N-terminal DNA-binding domain-like	8042713	3001820	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth A]	Topoisom_I_N_C	e1k4sA1	A: beta complex topology	X: Beta-strand domain in eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment (From Topology)	H: Beta-strand domain in eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment (From Topology)	T: Beta-strand domain in eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	F: Topoisom_I_N_C	ECOD (1.6)
D [auth A]	Topoisom_I_N	e1k4sA2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Topoisom_I_N	ECOD (1.6)
D [auth A]	Topo_C_assoc	e1k4sA3	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Topo_C_assoc	ECOD (1.6)
D [auth A]	Topoisom_I_N_N	e1k4sA4	A: alpha arrays	X: Alpha-helical domain in eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment (From Topology)	H: Alpha-helical domain in eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment (From Topology)	T: Alpha-helical domain in eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment	F: Topoisom_I_N_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	2.170.11.10	Mainly Beta	Beta Complex	DNA Topoisomerase I	domain 2	CATH (4.3.0)
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]	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
A [auth B]	5'-D(APAPAPAPAPGPAPCP(5IU)P(5IU))-3'	-	-	-
D [auth A]	DNA topoisomerase I	protein binding binding protein domain specific binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid 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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein binding binding protein domain specific binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid 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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding RNA 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 supercoiled DNA 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 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 DNA binding, bending single-stranded DNA binding	response to stimulus response to chemical response to xenobiotic stimulus nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process developmental process multicellular organism development multicellular organismal process embryonic cleavage response to stimulus response to chemical response to xenobiotic stimulus nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cellular process cell division embryo development rhythmic process circadian rhythm cell cycle chromosome segregation cell cycle process cell death programmed cell death chromosome organization DNA conformation change cellular component organization DNA topological change organelle organization cellular component organization or biogenesis regulation of biosynthetic process regulation of biological process regulation of cellular process circadian regulation of gene expression cellular biosynthetic process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process protein phosphorylation phosphorylation peptidyl-serine modification peptidyl-serine phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process chromatin organization chromatin remodeling	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle somatodendritic compartment cell body perikaryon neuronal cell body nucleoplasm chromosome fibrillar center protein-containing complex protein-DNA complex male germ cell nucleus germ cell nucleus cytoplasmic ribonucleoprotein granule ribonucleoprotein granule cytoplasm supramolecular complex P-body
B [auth C]	5'-D((SPT)PGPAPAPAPAPAP(5IU)P(5IU)P(5IU)P(5IU)PT)-3'	-	-	-
C [auth D]	5'-D(APAPAPAPAPTP(IDO)UP(IDO)UP(IDO)UP(IDO)UPCPAPAPAPGP(IDO)UPCP(IDO)UP(IDO)UP(IDO)UP(IDO)UPT)-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]	IPR013499	DNA topoisomerase I, eukaryotic-type	Domain
D [auth A]	IPR051062	DNA topoisomerase IB	Family
D [auth A]	IPR036202	DNA topoisomerase I, DNA binding, eukaryotic-type, N-terminal domain superfamily	Homologous Superfamily
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]	IPR013030	DNA topoisomerase I, DNA binding, N-terminal domain 2	Homologous Superfamily
D [auth A]	IPR018521	DNA topoisomerase I, active site	Active Site
D [auth A]	IPR013500	DNA topoisomerase I, catalytic core, eukaryotic-type	Domain
D [auth A]	IPR025834	Topoisomerase I C-terminal domain	Domain
D [auth A]	IPR013034	DNA topoisomerase I, DNA binding, N-terminal domain 1	Homologous Superfamily
D [auth A]	IPR014727	DNA topoisomerase I, catalytic core, alpha/beta subdomain	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
A [auth B]	5IU	Parent Component: DU
D [auth A]	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048
B [auth C]	5IU	Parent Component: DU RESID: AA0039
B [auth C]	SPT	Parent Component: DT RESID: AA0039
C [auth D]	5IU	Parent Component: DU 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.