Structure of PDB 6rkv Chain B Binding Site BS01

Receptor Information

>6rkv Chain B (length=381) Species: 83333 (Escherichia coli K-12)

GLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKIL
NVEKARFDKMLSSQEVATLITALYNPDKLRYHSIIIMTDADVDGSHIRTL
LLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISI
ALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKEL
IYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNL
FEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIER
GERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPES
RRMLRVTVKDAIAADQLFTTLMGDAVEPRRA

Ligand information

>6rkv Chain G (length=18)

gtacctacggcttatgat

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rkv Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.
• Resolution: 4.6 Å
• Binding residue (original residue number in PDB): L451 N452 K455 L780
• Binding residue (residue number reindexed from 1): L50 N51 K54 L371

Enzymatic activity

• Enzyme Commision number: 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

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

External links

• PDB: RCSB:6rkv, PDBe:6rkv, PDBj:6rkv
• PDBsum: 6rkv
• PubMed: 31666516
• UniProt: P0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)