3L4K | pdb_00003l4k

Topoisomerase II-DNA cleavage complex, metal-bound

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3l4ka_	Multi-domain proteins (alpha and beta)	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	automated matches	brewer's yeast,lager beer yeast,yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Type II DNA topoisomerase half-clamp domain-like	8037554	3001800	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8055747	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Toprim domain-like	8055749	3000737	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)
A		e3l4kA1	A: OB-fold	X: Rubredoxin-related	H: Rubredoxin-related	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.1490.30	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
A	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family
A	PF16898	C-terminal associated domain of TOPRIM (TOPRIM_C)	C-terminal associated domain of TOPRIM	-	Family
A	PF00521	DNA gyrase/topoisomerase IV, subunit A (DNA_topoisoIV)	DNA gyrase/topoisomerase IV, subunit A	This entry represents a domain found in type IIA topoisomerases, such as bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA), and mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that r ...	This entry represents a domain found in type IIA topoisomerases, such as bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA), and mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	DNA (5'-D(CPGPCPGPAPAPTPCPGPTPCPAPTPCP*C)-3')	-	-	-
D	DNA (5'-D(PGPGPAPTPGPAPCPGPAPTP*)-3')	-	-	-
C	DNA (5'-D(CPGPCPGPGPTPAPGPCPAPGPTPAPGP*G)-3')	-	-	-
B	DNA (5'-D(PCPCPTPAPCPTPGPCPTPAP*C)-3')	-	-	-
A	DNA topoisomerase 2	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 ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA topoisomerase activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity catalytic activity macromolecular conformation isomerase activity ATP-dependent activity cation binding metal ion binding identical protein binding protein binding	homologous recombination sexual reproduction reproductive process meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process DNA recombination meiotic cell cycle homologous recombination sexual reproduction reproductive process meiotic cell cycle process nucleobase-containing compound metabolic process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process DNA recombination meiotic cell cycle organelle fission primary metabolic process DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process metabolic process cellular process macromolecule metabolic process resolution of meiotic recombination intermediates mitotic recombination telomere organization chromosome organization telomere maintenance telomere maintenance via recombination DNA conformation change DNA topological change organelle assembly protein-containing complex organization membraneless organelle assembly CENP-A containing chromatin assembly cellular component biogenesis cellular component assembly chromatin organization kinetochore assembly protein-containing complex assembly kinetochore organization regulation of DNA recombination regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process regulation of mitotic recombination regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA metabolic process DNA-templated DNA replication DNA strand elongation DNA replication DNA strand elongation involved in DNA replication replication fork progression beyond termination site regulation of DNA replication termination DNA replication termination regulation of DNA-templated DNA replication regulation of DNA replication RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process rRNA transcription rRNA metabolic process nuclear chromosome segregation sister chromatid segregation chromosome segregation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle DNA replication termination region membraneless organelle intracellular membraneless organelle chromosome condensed nuclear chromosome nucleus membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle DNA replication termination region membraneless organelle intracellular membraneless organelle chromosome condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome intracellular organelle lumen organelle lumen synaptonemal structure synaptonemal complex condensed chromosome nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001154	DNA topoisomerase II, eukaryotic-type	Family
A	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
A	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
A	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A	IPR006171	TOPRIM domain	Domain
A	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A	IPR034157	DNA topoisomerase 2, TOPRIM domain	Domain
A	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A	IPR001241	DNA topoisomerase, type IIA	Family
A	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
A	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
A	IPR031660	C-terminal associated domain of TOPRIM	Domain
A	IPR050634	DNA Topoisomerase II	Family
A	IPR002205	DNA topoisomerase, type IIA, domain A	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048

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.