5NPK | pdb_00005npk

1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth d]	DNA_topoisoIV_1st	e5npkd1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
F [auth d]	DNA_topoisoIV_3rd	e5npkd3	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 [auth d]	DNA_topoisoIV_2nd_1	e5npkd4	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 [auth d]	DNA_gyraseB_C	e5npkd2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
E [auth b]	DNA_topoisoIV_1st	e5npkb5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
E [auth b]	DNA_topoisoIV_3rd	e5npkb4	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)
E [auth b]	DNA_topoisoIV_2nd_1	e5npkb3	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)
E [auth b]	DNA_gyraseB_C	e5npkb2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
B [auth D]	DNA_topoisoIV_1st	e5npkD4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
B [auth D]	DNA_topoisoIV_3rd	e5npkD1	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)
B [auth D]	DNA_topoisoIV_2nd_1	e5npkD2	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)
B [auth D]	DNA_gyraseB_C	e5npkD3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)
A [auth B]	DNA_topoisoIV_1st	e5npkB3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A [auth B]	DNA_topoisoIV_3rd	e5npkB2	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 [auth B]	DNA_topoisoIV_2nd_1	e5npkB1	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 [auth B]	DNA_gyraseB_C	e5npkB4	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
F [auth d]	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (utative)
E [auth b]	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (utative)
B [auth D]	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (utative)
A [auth B]	3.40.50.670	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F], G [auth e], H [auth f]	DNA (5'-D(APGPCPCPGPTPAPGPGPTPAPCPCPTPAPCPGPGPCPT)-3')	-	-	-
A [auth B], B [auth D], E [auth b], F [auth d]	DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A	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 response to stimulus response to chemical response to antibiotic	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome cytoplasm 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 [auth B], B [auth D], E [auth b], F [auth d]	IPR011557	DNA gyrase, subunit B	Family
A [auth B], B [auth D], E [auth b], F [auth d]	IPR034160	DNA gyrase subunit B, TOPRIM domain	Domain
A [auth B], B [auth D], E [auth b], F [auth d]	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
A [auth B], B [auth D], E [auth b], F [auth d]	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
A [auth B], B [auth D], E [auth b], F [auth d]	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR006171	TOPRIM domain	Domain
A [auth B], B [auth D], E [auth b], F [auth d]	IPR000565	DNA topoisomerase, type IIA, subunit B	Family
A [auth B], B [auth D], E [auth b], F [auth d]	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR001241	DNA topoisomerase, type IIA	Family
A [auth B], B [auth D], E [auth b], F [auth d]	IPR002288	DNA gyrase B subunit, C-terminal	Domain
A [auth B], B [auth D], E [auth b], F [auth d]	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR035516	DNA gyrase/topoisomerase IV, subunit A, C-terminal	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR050220	Type II DNA Topoisomerases	Family
A [auth B], B [auth D], E [auth b], F [auth d]	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A [auth B], B [auth D], E [auth b], F [auth d]	IPR005743	DNA gyrase, subunit A	Family
A [auth B], B [auth D], E [auth b], F [auth d]	IPR006691	DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat	Repeat
A [auth B], B [auth D], E [auth b], F [auth d]	IPR002205	DNA topoisomerase, type IIA, domain A	Domain