Structure of PDB 6fm4 Chain B Binding Site BS01

Receptor Information

>6fm4 Chain B (length=672) Species: 158879 (Staphylococcus aureus subsp. aureus N315)

KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEK
ARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHI
RTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANERNITSEMR
ESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSAR
IVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAA
AMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLA
NGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFP
TAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVN
KARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILN
NLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQY
NLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSE
KQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLV
RDELTEIRDRFGDDRRTEIQLG

Ligand information

>6fm4 Chain E (length=19)

gccgtagggccctacggct

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fm4 Virtual Screening Approach and Investigation of Structure-Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): E435 D437 S438 R458 G459 K460 D508 D512 R1033 H1046 H1079 H1081 G1082 S1085 R1092 I1175 R1272
• Binding residue (residue number reindexed from 1): E19 D21 S22 R42 G43 K44 D92 D96 R214 H227 H260 H262 G263 S266 R273 I356 R453

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
• GO:0005524 ATP binding

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006265 DNA topological change

External links

• PDB: RCSB:6fm4, PDBe:6fm4, PDBj:6fm4
• PDBsum: 6fm4
• PubMed: 31276392
• UniProt: P66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
  Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)