Structure of PDB 6fm4 Chain D Binding Site BS01

Receptor Information

>6fm4 Chain D (length=670) Species: 158879 (Staphylococcus aureus subsp. aureus N315)

KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEK
ARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHI
RTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMRE
SFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARI
VGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAA
MRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLAN
GASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPT
AGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNK
ARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNN
LYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYN
LRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEK
QAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVR
DELTEIRDRFGDDRRTEIQL

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): K460 L462 N463 K466 R471 H515 R629 R1122 F1123 I1175 G1178 M1179 R1238 S1330
• Binding residue (residue number reindexed from 1): K44 L46 N47 K50 R55 H99 R179 R302 F303 I355 G358 M359 R418 S510

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)