4CKK | pdb_00004ckk

Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d4ckkd_	Multi-domain proteins (alpha and beta)	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	DNA Gyrase A	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d4ckkc_	Multi-domain proteins (alpha and beta)	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	DNA Gyrase A	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d4ckkb_	Multi-domain proteins (alpha and beta)	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	DNA Gyrase A	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d4ckka_	Multi-domain proteins (alpha and beta)	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	Type II DNA topoisomerase C-terminal domain-like	DNA Gyrase A	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Ribosomal_S27	e4ckkD4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: Ribosomal_S27	ECOD (v294.1)
D	DNA_topoisoIV	e4ckkD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DNA_topoisoIV	ECOD (v294.1)
C	Peptidase_M10	e4ckkC1	A: a/b three-layered sandwiches	X: Single-stranded left-handed beta-helix	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_M10	ECOD (v294.1)
C	Ribosomal_S27	e4ckkC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: Ribosomal_S27	ECOD (v294.1)
B	Ribosomal_S27	e4ckkB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: Ribosomal_S27	ECOD (v294.1)
B	DNA_topoisoIV	e4ckkB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DNA_topoisoIV	ECOD (v294.1)
A	Ribosomal_S27	e4ckkA5	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: Ribosomal_S27	ECOD (v294.1)
A	DNA_topoisoIV	e4ckkA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: DNA_topoisoIV	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
D	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)
C	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
C	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)
B	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
B	3.30.1360.40	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)
A	3.90.199.10	Alpha Beta	Alpha-Beta Complex	Topoisomerase II	domain 5	CATH (4.3.0)
A	1.10.268.10	Mainly Alpha	Orthogonal Bundle	Topoisomerase	domain 3	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	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	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 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	IPR035516	DNA gyrase/topoisomerase IV, subunit A, C-terminal	Homologous Superfamily
A, B, C, D	IPR050220	Type II DNA Topoisomerases	Family
A, B, C, D	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A, B, C, D	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A, B, C, D	IPR005743	DNA gyrase, subunit A	Family
A, B, C, D	IPR006691	DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat	Repeat
A, B, C, D	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.