Structure of PDB 6rku Chain D

Receptor sequence
>6rkuD (length=381) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
GLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKIL
NVEKARFDKMLSSQEVATLITALYNPDKLRYHSIIIMTDADVDGSHIRTL
LLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISI
ALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKEL
IYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNL
FEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIER
GERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPES
RRMLRVTVKDAIAADQLFTTLMGDAVEPRRA
3D structure
PDB6rku Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.
ChainD
Resolution4.0 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna D K449 D502 K48 D93
BS02 dna D K406 E424 D426 K5 E23 D25
BS03 dna D L451 K455 L780 L50 K54 L371
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003916 DNA topoisomerase activity
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0034335 DNA negative supercoiling activity
GO:0046872 metal ion binding
Biological Process
GO:0006261 DNA-templated DNA replication
GO:0006265 DNA topological change
GO:0006351 DNA-templated transcription
GO:0009410 response to xenobiotic stimulus
GO:0046677 response to antibiotic
GO:0051276 chromosome organization
Cellular Component
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009330 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex

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Molecular Function
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Cellular Component
External links
PDB RCSB:6rku, PDBe:6rku, PDBj:6rku
PDBsum6rku
PubMed31666516
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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