Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help
SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9GDB

RNAP-TopoI complex on bubble scaffold - consensus reconstruction

This is a non-PDB format compatible entry.
Functional Information from GO Data
ChainGOidnamespacecontents
A0000428cellular_componentDNA-directed RNA polymerase complex
A0003677molecular_functionDNA binding
A0003899molecular_functionDNA-directed RNA polymerase activity
A0005515molecular_functionprotein binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006351biological_processDNA-templated transcription
A0006352biological_processDNA-templated transcription initiation
A0006879biological_processintracellular iron ion homeostasis
A0009408biological_processresponse to heat
A0016020cellular_componentmembrane
A0016740molecular_functiontransferase activity
A0016779molecular_functionnucleotidyltransferase activity
A0031564biological_processtranscription antitermination
A0032784biological_processregulation of DNA-templated transcription elongation
A0034062molecular_function5'-3' RNA polymerase activity
A0036460biological_processcellular response to cell envelope stress
A0042128biological_processnitrate assimilation
A0044780biological_processbacterial-type flagellum assembly
A0048870biological_processcell motility
A0071973biological_processbacterial-type flagellum-dependent cell motility
A0090605biological_processsubmerged biofilm formation
A2000142biological_processregulation of DNA-templated transcription initiation
B0000428cellular_componentDNA-directed RNA polymerase complex
B0003677molecular_functionDNA binding
B0003899molecular_functionDNA-directed RNA polymerase activity
B0005515molecular_functionprotein binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006351biological_processDNA-templated transcription
B0006352biological_processDNA-templated transcription initiation
B0006879biological_processintracellular iron ion homeostasis
B0009408biological_processresponse to heat
B0016020cellular_componentmembrane
B0016740molecular_functiontransferase activity
B0016779molecular_functionnucleotidyltransferase activity
B0031564biological_processtranscription antitermination
B0032784biological_processregulation of DNA-templated transcription elongation
B0034062molecular_function5'-3' RNA polymerase activity
B0036460biological_processcellular response to cell envelope stress
B0042128biological_processnitrate assimilation
B0044780biological_processbacterial-type flagellum assembly
B0048870biological_processcell motility
B0071973biological_processbacterial-type flagellum-dependent cell motility
B0090605biological_processsubmerged biofilm formation
B2000142biological_processregulation of DNA-templated transcription initiation
C0000345cellular_componentcytosolic DNA-directed RNA polymerase complex
C0000428cellular_componentDNA-directed RNA polymerase complex
C0003677molecular_functionDNA binding
C0003899molecular_functionDNA-directed RNA polymerase activity
C0005515molecular_functionprotein binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006351biological_processDNA-templated transcription
C0006352biological_processDNA-templated transcription initiation
C0006354biological_processDNA-templated transcription elongation
C0006879biological_processintracellular iron ion homeostasis
C0009408biological_processresponse to heat
C0016020cellular_componentmembrane
C0016740molecular_functiontransferase activity
C0016779molecular_functionnucleotidyltransferase activity
C0031564biological_processtranscription antitermination
C0032784biological_processregulation of DNA-templated transcription elongation
C0034062molecular_function5'-3' RNA polymerase activity
C0036460biological_processcellular response to cell envelope stress
C0042128biological_processnitrate assimilation
C0044780biological_processbacterial-type flagellum assembly
C0046677biological_processresponse to antibiotic
C0048870biological_processcell motility
C0071973biological_processbacterial-type flagellum-dependent cell motility
C0090605biological_processsubmerged biofilm formation
C2000142biological_processregulation of DNA-templated transcription initiation
D0000287molecular_functionmagnesium ion binding
D0000428cellular_componentDNA-directed RNA polymerase complex
D0003677molecular_functionDNA binding
D0003899molecular_functionDNA-directed RNA polymerase activity
D0005515molecular_functionprotein binding
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006351biological_processDNA-templated transcription
D0006352biological_processDNA-templated transcription initiation
D0006879biological_processintracellular iron ion homeostasis
D0008270molecular_functionzinc ion binding
D0009408biological_processresponse to heat
D0016020cellular_componentmembrane
D0016740molecular_functiontransferase activity
D0016779molecular_functionnucleotidyltransferase activity
D0031564biological_processtranscription antitermination
D0032784biological_processregulation of DNA-templated transcription elongation
D0034062molecular_function5'-3' RNA polymerase activity
D0036460biological_processcellular response to cell envelope stress
D0042128biological_processnitrate assimilation
D0044780biological_processbacterial-type flagellum assembly
D0046677biological_processresponse to antibiotic
D0046872molecular_functionmetal ion binding
D0048870biological_processcell motility
D0071973biological_processbacterial-type flagellum-dependent cell motility
D0090605biological_processsubmerged biofilm formation
D2000142biological_processregulation of DNA-templated transcription initiation
E0000345cellular_componentcytosolic DNA-directed RNA polymerase complex
E0000428cellular_componentDNA-directed RNA polymerase complex
E0001000molecular_functionbacterial-type RNA polymerase core enzyme binding
E0003677molecular_functionDNA binding
E0003899molecular_functionDNA-directed RNA polymerase activity
E0005829cellular_componentcytosol
E0006351biological_processDNA-templated transcription
E0006352biological_processDNA-templated transcription initiation
E0006879biological_processintracellular iron ion homeostasis
E0009408biological_processresponse to heat
E0016740molecular_functiontransferase activity
E0016779molecular_functionnucleotidyltransferase activity
E0030880cellular_componentRNA polymerase complex
E0031564biological_processtranscription antitermination
E0032784biological_processregulation of DNA-templated transcription elongation
E0034062molecular_function5'-3' RNA polymerase activity
E0036460biological_processcellular response to cell envelope stress
E0042128biological_processnitrate assimilation
E0044780biological_processbacterial-type flagellum assembly
E0048870biological_processcell motility
E0065003biological_processprotein-containing complex assembly
E0071973biological_processbacterial-type flagellum-dependent cell motility
E0090605biological_processsubmerged biofilm formation
E2000142biological_processregulation of DNA-templated transcription initiation
F0003677molecular_functionDNA binding
F0003916molecular_functionDNA topoisomerase activity
F0003917molecular_functionDNA topoisomerase type I (single strand cut, ATP-independent) activity
F0005515molecular_functionprotein binding
F0005829cellular_componentcytosol
F0006265biological_processDNA topological change
F0007059biological_processchromosome segregation
F0008270molecular_functionzinc ion binding
F0016853molecular_functionisomerase activity
F0046872molecular_functionmetal ion binding
F0140226molecular_functionRNA topoisomerase activity
Functional Information from PROSITE/UniProt
site_idPS01166
Number of Residues13
DetailsRNA_POL_BETA RNA polymerases beta chain signature. GdKMAGrHGNKGV
ChainResidueDetails
CGLY1063-VAL1075
site_idPS00396
Number of Residues15
DetailsTOPO_IA_1 Topoisomerase (Topo) IA-type active site signature. QrLYEagy.........ITYmRTD
ChainResidueDetails
FGLN309-ASP323
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
DetailsRegion: {"description":"Required for interaction with Crp at class II promoters"}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues11
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"32871103","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4MEX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4MEY","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"HAMAP-Rule","id":"MF_01322","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues417
DetailsDomain: {"description":"Topo IA-type catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01383","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues31
DetailsZinc finger: {"description":"C4-type 1"}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues27
DetailsZinc finger: {"description":"C4-type 2"}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues25
DetailsZinc finger: {"description":"C4-type 3"}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues5
DetailsRegion: {"description":"Interaction with DNA"}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues1
DetailsActive site: {"description":"O-(5'-phospho-DNA)-tyrosine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU01383","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21482796","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8114910","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9497321","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00952","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues8
DetailsSite: {"description":"Interaction with DNA"}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues7
DetailsM-CSA 366
ChainResidueDetails
FGLU9electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, metal ligand, proton acceptor, proton donor, proton relay
FASP111electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, metal ligand, proton acceptor, proton donor, proton relay
FASP113metal ligand
FGLU115metal ligand
FTYR319activator, covalently attached, hydrogen bond acceptor, nucleofuge, nucleophile, proton acceptor, proton donor
FARG321electrostatic stabiliser
FHIS365electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, proton acceptor, proton donor

246905

PDB entries from 2025-12-31

PDB statisticsPDBj update infoContact PDBjnumon