Structure of PDB 7z9k Chain D Binding Site BS01

Receptor Information

>7z9k Chain D (length=402) Species: 511145 (Escherichia coli str. K-12 substr. MG1655)

GKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVE
KARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGS
HIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQ
YQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKA
MLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTN
AEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEED
AFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETT
MDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI
EN

Ligand information

>7z9k Chain F (length=14)

agaatcaggcataa

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7z9k Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin.
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): E424 R457 D502
• Binding residue (residue number reindexed from 1): E20 R53 D98

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:7z9k, PDBe:7z9k, PDBj:7z9k
• PDBsum: 7z9k
• PubMed: 36741192
• UniProt: P0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)