Annotations: 4GFH

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8039160	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type II DNA topoisomerase half-clamp domain-like	8037554	3001800	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Toprim domain-like	8055749	3000737	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8039165	3000091	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8055747	3000034	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8039160	3000100	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Toprim domain-like	8055749	3000737	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Type II DNA topoisomerase half-clamp domain-like	8037554	3001800	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8039165	3000091	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Winged helix DNA-binding domain	8055747	3000034	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	DNA_topoisoIV_1st	e4gfhA4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A	DNA_topoisoIV_3rd	e4gfhA1	A: alpha bundles	X: alpha-helical domain in type II DNA topoisomerase (From Topology)	H: alpha-helical domain in type II DNA topoisomerase (From Topology)	T: alpha-helical domain in type II DNA topoisomerase	F: DNA_topoisoIV_3rd	ECOD (1.6)
A	DNA_gyraseB	e4gfhA3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: DNA_gyraseB	ECOD (1.6)
A	HATPase_c_1	e4gfhA5	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_1	ECOD (1.6)
A	DNA_topoisoIV_2nd_1	e4gfhA2	A: a+b two layers	X: a+b domain in type II DNA topoisomerase (From Topology)	H: a+b domain in type II DNA topoisomerase (From Topology)	T: a+b domain in type II DNA topoisomerase	F: DNA_topoisoIV_2nd_1	ECOD (1.6)
A	DNA_gyraseB_C	e4gfhA6	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
F	DNA_topoisoIV_1st	e4gfhF6	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
F	DNA_topoisoIV_3rd	e4gfhF5	A: alpha bundles	X: alpha-helical domain in type II DNA topoisomerase (From Topology)	H: alpha-helical domain in type II DNA topoisomerase (From Topology)	T: alpha-helical domain in type II DNA topoisomerase	F: DNA_topoisoIV_3rd	ECOD (1.6)
F	DNA_gyraseB	e4gfhF4	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: DNA_gyraseB	ECOD (1.6)
F	HATPase_c_1	e4gfhF1	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_1	ECOD (1.6)
F	DNA_topoisoIV_2nd_1	e4gfhF3	A: a+b two layers	X: a+b domain in type II DNA topoisomerase (From Topology)	H: a+b domain in type II DNA topoisomerase (From Topology)	T: a+b domain in type II DNA topoisomerase	F: DNA_topoisoIV_2nd_1	ECOD (1.6)
F	DNA_gyraseB_C	e4gfhF7	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F	PF00204	DNA gyrase B (DNA_gyraseB)	DNA gyrase B	This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.	Domain
A, F	PF02518	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (HATPase_c)	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.	Domain
A, F	PF16898	C-terminal associated domain of TOPRIM (TOPRIM_C)	C-terminal associated domain of TOPRIM	-	Family
A, F	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family
A, F	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
A, F	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 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 chromatin organization chromatin remodeling chromatin remodeling at centromere 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
B, G	DNA (5'-D(PCPCPTPAPCPTPGPCPTPAP*C)-3')	-	-	-
C, H	DNA (5'-D(CPGPCPGPGPTPAPGPCPAPGPTPAPGP*G)-3')	-	-	-
D, I	DNA (5'-D(PGPGPAPTPGPAPCPGPAPTP*(TSP))-3')	-	-	-
E, J	DNA (5'-D(CPGPCPGPAPAPTPCPGPTPCPAPTPCP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, F	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048
D, I	TSP	Parent Component: DT 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.