1QZR | pdb_00001qzr

CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE)

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)
B	d1qzrb1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	DNA topoisomerase II	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1qzrb2	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	DNA topoisomerase II	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1qzra1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	DNA topoisomerase II	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1qzra2	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	DNA topoisomerase II	baker's 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)
B	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8039165	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8039160	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8039160	3000100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8039165	3000091	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)
B	Staphylokinase	e1qzrB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)
B	Aminotran_4	e1qzrB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Aminotran_4	ECOD (v294.1)
A	Staphylokinase	e1qzrA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Staphylokinase	ECOD (v294.1)
A	Aminotran_4	e1qzrA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Aminotran_4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
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	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	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, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA topoisomerase II	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, B	IPR001154	DNA topoisomerase II, eukaryotic-type	Family
A, B	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
A, B	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
A, B	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A, B	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A, B	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B	IPR006171	TOPRIM domain	Domain
A, B	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A, B	IPR034157	DNA topoisomerase 2, TOPRIM domain	Domain
A, B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B	IPR001241	DNA topoisomerase, type IIA	Family
A, B	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
A, B	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A, B	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
A, B	IPR031660	C-terminal associated domain of TOPRIM	Domain
A, B	IPR050634	DNA Topoisomerase II	Family
A, B	IPR002205	DNA topoisomerase, type IIA, domain A	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.