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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6RKW

CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0003677molecular_functionDNA binding
A0003916molecular_functionDNA topoisomerase activity
A0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005694cellular_componentchromosome
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006259biological_processDNA metabolic process
A0006261biological_processDNA-templated DNA replication
A0006265biological_processDNA topological change
A0006351biological_processDNA-templated transcription
A0008094molecular_functionATP-dependent activity, acting on DNA
A0009330cellular_componentDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
A0009410biological_processresponse to xenobiotic stimulus
A0016020cellular_componentmembrane
A0016853molecular_functionisomerase activity
A0034335molecular_functionDNA negative supercoiling activity
A0042802molecular_functionidentical protein binding
A0046677biological_processresponse to antibiotic
A0051276biological_processchromosome organization
A2000104biological_processnegative regulation of DNA-templated DNA replication
B0000166molecular_functionnucleotide binding
B0003677molecular_functionDNA binding
B0003916molecular_functionDNA topoisomerase activity
B0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005694cellular_componentchromosome
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006261biological_processDNA-templated DNA replication
B0006265biological_processDNA topological change
B0006351biological_processDNA-templated transcription
B0008094molecular_functionATP-dependent activity, acting on DNA
B0009330cellular_componentDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
B0009410biological_processresponse to xenobiotic stimulus
B0016853molecular_functionisomerase activity
B0034335molecular_functionDNA negative supercoiling activity
B0046677biological_processresponse to antibiotic
B0046872molecular_functionmetal ion binding
B0051276biological_processchromosome organization
C0000166molecular_functionnucleotide binding
C0003677molecular_functionDNA binding
C0003916molecular_functionDNA topoisomerase activity
C0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005694cellular_componentchromosome
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006259biological_processDNA metabolic process
C0006261biological_processDNA-templated DNA replication
C0006265biological_processDNA topological change
C0006351biological_processDNA-templated transcription
C0008094molecular_functionATP-dependent activity, acting on DNA
C0009330cellular_componentDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
C0009410biological_processresponse to xenobiotic stimulus
C0016020cellular_componentmembrane
C0016853molecular_functionisomerase activity
C0034335molecular_functionDNA negative supercoiling activity
C0042802molecular_functionidentical protein binding
C0046677biological_processresponse to antibiotic
C0051276biological_processchromosome organization
C2000104biological_processnegative regulation of DNA-templated DNA replication
D0000166molecular_functionnucleotide binding
D0003677molecular_functionDNA binding
D0003916molecular_functionDNA topoisomerase activity
D0003918molecular_functionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005694cellular_componentchromosome
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006261biological_processDNA-templated DNA replication
D0006265biological_processDNA topological change
D0006351biological_processDNA-templated transcription
D0008094molecular_functionATP-dependent activity, acting on DNA
D0009330cellular_componentDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
D0009410biological_processresponse to xenobiotic stimulus
D0016853molecular_functionisomerase activity
D0034335molecular_functionDNA negative supercoiling activity
D0046677biological_processresponse to antibiotic
D0046872molecular_functionmetal ion binding
D0051276biological_processchromosome organization
Functional Information from PDB Data
site_idAC1
Number of Residues18
Detailsbinding site for residue ANP B 901
ChainResidue
BGLU42
BGLY114
BLEU115
BHIS116
BGLY117
BVAL118
BGLY119
BVAL120
BGLN335
DILE10
BASN46
BILE78
BILE94
BALA100
BGLY101
BGLY102
BLYS103
BTYR109
site_idAC2
Number of Residues19
Detailsbinding site for residue ANP D 901
ChainResidue
BTYR5
DGLU42
DASN46
DALA47
DGLU50
DASP73
DILE78
DILE94
DALA100
DGLY102
DLYS103
DTYR109
DGLY114
DLEU115
DHIS116
DGLY117
DVAL118
DGLY119
DVAL120
site_idAC3
Number of Residues10
Detailsbinding site for residue JHN G 101
ChainResidue
AALA67
AASP82
AMET120
CALA67
CASP82
CMET120
GDT2
GDA3
HDT2
HDA3
Functional Information from PROSITE/UniProt
site_idPS00177
Number of Residues9
DetailsTOPOISOMERASE_II DNA topoisomerase II signature. LVEGDSAGG
ChainResidueDetails
BLEU422-GLY430
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues620
DetailsRegion: {"description":"C-terminal domain (CTD)","evidences":[{"source":"PubMed","id":"15897198","evidenceCode":"ECO:0000303"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues12
DetailsMotif: {"description":"GyrA-box","evidences":[{"source":"HAMAP-Rule","id":"MF_01897","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9426128","evidenceCode":"ECO:0000303"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues2
DetailsActive site: {"description":"O-(5'-phospho-DNA)-tyrosine intermediate","evidences":[{"source":"HAMAP-Rule","id":"MF_01897","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"3031051","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues436
DetailsRegion: {"description":"ATPase domain","evidences":[{"source":"PubMed","id":"10734094","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"1646964","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues342
DetailsRegion: {"description":"Transducer domain","evidences":[{"source":"PubMed","id":"10734094","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"1646964","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues2
DetailsActive site: {"description":"Proton acceptor (ATPase activity)","evidences":[{"source":"PubMed","id":"10734094","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"8248233","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"25202966","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25849408","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10734094","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues18
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"10734094","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25202966","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25849408","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues14
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"25849408","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"10734094","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25849408","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01898","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"12051843","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"18642932","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsSite: {"description":"Transition state stabilizer","evidences":[{"source":"PubMed","id":"9657678","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues4
DetailsSite: {"description":"Interaction with DNA","evidences":[{"source":"HAMAP-Rule","id":"MF_01898","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues3
DetailsM-CSA 745
ChainResidueDetails
AARG32electrostatic stabiliser
AHIS78proton acceptor
ATYR122metal ligand, nucleofuge, nucleophile, proton acceptor, proton donor
site_idMCSA2
Number of Residues3
DetailsM-CSA 745
ChainResidueDetails
BASP32electrostatic stabiliser
BILE78proton acceptor
BVAL122metal ligand, nucleofuge, nucleophile, proton acceptor, proton donor

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PDB entries from 2025-10-22

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