1KIJ | pdb_00001kij

Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin

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	d1kijb1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	DNA gyrase B	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1kijb2	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 gyrase B	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1kija1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	DNA gyrase/MutL, second domain	DNA gyrase B	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1kija2	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 gyrase B	(Thermus thermophilus ) [TaxId: 274 ],	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	8040316	3000091	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8040314	3000100	SCOP2B (2022-06-29)
A	SCOP2 Family	DNA gyrase/MutL transducer domain-like	8027935	4000187	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA gyrase/MutL ATPase domain-like	8027937	4000168	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosomal protein S5 domain 2-like	8040314	3000100	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8040316	3000091	SCOP2 (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	e1kijB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
B	Aminotran_4	e1kijB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Aminotran_4	ECOD (develop294)
A	Staphylokinase	e1kijA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
A	Aminotran_4	e1kijA2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Aminotran_4	ECOD (develop294)

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 GYRASE SUBUNIT B	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 nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA negative supercoiling activity catalytic activity, acting on DNA DNA topoisomerase activity catalytic activity macromolecular conformation isomerase activity cation binding metal ion binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process chromosome organization DNA conformation change cellular component organization DNA topological change organelle organization nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process chromosome organization DNA conformation change cellular component organization DNA topological change organelle organization cellular component organization or biogenesis	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011557	DNA gyrase, subunit B	Family
A, B	IPR034160	DNA gyrase subunit B, TOPRIM domain	Domain
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	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B	IPR006171	TOPRIM domain	Domain
A, B	IPR000565	DNA topoisomerase, type IIA, subunit B	Family
A, B	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A, B	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
A, B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B	IPR001241	DNA topoisomerase, type IIA	Family
A, B	IPR002288	DNA gyrase B subunit, C-terminal	Domain
A, B	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily

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.