1MX0

Structure of topoisomerase subunit

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	d1mx0a1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Topoisomerase VI-B subunit middle domain	Topoisomerase VI-B subunit middle domain	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
A	d1mx0a2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
A	d1mx0a3	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	DNA gyrase/MutL, N-terminal domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
B	d1mx0b1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Topoisomerase VI-B subunit middle domain	Topoisomerase VI-B subunit middle domain	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
B	d1mx0b2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
B	d1mx0b3	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	DNA gyrase/MutL, N-terminal domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
C	d1mx0c1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Topoisomerase VI-B subunit middle domain	Topoisomerase VI-B subunit middle domain	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
C	d1mx0c2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
C	d1mx0c3	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	DNA gyrase/MutL, N-terminal domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
D	d1mx0d1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Topoisomerase VI-B subunit middle domain	Topoisomerase VI-B subunit middle domain	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
D	d1mx0d2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
D	d1mx0d3	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	DNA gyrase/MutL, N-terminal domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
E	d1mx0e1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Topoisomerase VI-B subunit middle domain	Topoisomerase VI-B subunit middle domain	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
E	d1mx0e2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
E	d1mx0e3	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	DNA gyrase/MutL, N-terminal domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
F	d1mx0f1	All alpha proteins	S13-like H2TH domain	S13-like H2TH domain	Topoisomerase VI-B subunit middle domain	Topoisomerase VI-B subunit middle domain	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
F	d1mx0f2	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)
F	d1mx0f3	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	DNA gyrase/MutL, N-terminal domain	Topoisomerase VI-B subunit	(Saccharolobus shibatae ) [TaxId: 2286 ],	SCOPe (2.08)

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	8003724	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	S13-like H2TH domain	8003720	3000053	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8003716	3000091	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8003724	3000100	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	FbpA_2nd_1	e1mx0A1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
A	Topo-VIb_trans	e1mx0A2	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: Topo-VIb_trans	ECOD (1.6)
A	HATPase_c_3	e1mx0A3	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_3	ECOD (1.6)
B	FbpA_2nd_1	e1mx0B1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
B	Topo-VIb_trans	e1mx0B2	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: Topo-VIb_trans	ECOD (1.6)
B	HATPase_c_3	e1mx0B3	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_3	ECOD (1.6)
C	FbpA_2nd_1	e1mx0C1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
C	Topo-VIb_trans	e1mx0C2	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: Topo-VIb_trans	ECOD (1.6)
C	HATPase_c_3	e1mx0C3	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_3	ECOD (1.6)
D	FbpA_2nd_1	e1mx0D1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
D	Topo-VIb_trans	e1mx0D2	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: Topo-VIb_trans	ECOD (1.6)
D	HATPase_c_3	e1mx0D3	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_3	ECOD (1.6)
E	FbpA_2nd_1	e1mx0E1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
E	Topo-VIb_trans	e1mx0E2	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: Topo-VIb_trans	ECOD (1.6)
E	HATPase_c_3	e1mx0E3	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_3	ECOD (1.6)
F	FbpA_2nd_1	e1mx0F1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: FbpA_2nd_1	ECOD (1.6)
F	Topo-VIb_trans	e1mx0F2	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: Topo-VIb_trans	ECOD (1.6)
F	HATPase_c_3	e1mx0F3	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_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
A	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
B	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
B	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
C	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
D	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
D	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
E	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
E	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
F	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
F	1.10.8.50	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
F	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, 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, B, C, D, E A, B, C, D, E, F	PF09239	Topoisomerase VI B subunit, transducer (Topo-VIb_trans)	Topoisomerase VI B subunit, transducer	Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to ...	Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Type II DNA topoisomerase VI subunit B	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 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 ATP-dependent activity identical protein binding protein binding	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 cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process DNA duplex unwinding 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 cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process DNA duplex unwinding DNA-templated DNA replication DNA geometric change DNA unwinding involved in DNA replication DNA replication	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050761	TOP6B	Unknown
A, B, C, D, E A, B, C, D, E, F	IPR005734	DNA topoisomerase VI, subunit B	Family
A, B, C, D, E A, B, C, D, E, F	IPR015320	DNA topoisomerase VI, subunit B, transducer	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.