Structure of PDB 5npk Chain D Binding Site BS01

Receptor Information

>5npk Chain D (length=674) Species: 158879 (Staphylococcus aureus subsp. aureus N315)

KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEK
ARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHI
RTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLNERNITSE
MRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKS
ARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDG
AAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNL
LANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPD
FPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQ
VNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVI
LNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRT
QYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKL
SEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQ
LVRDELTEIRDRFGDDRRTEIQLG

Ligand information

>5npk Chain E (length=17)

agccgtagcctacggct

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5npk Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
• Resolution: 1.98 Å
• Binding residue (original residue number in PDB): K460 L462 N463 K466 R471 H515 V626 R629 I1175 G1178 M1179 R1238 S1330
• Binding residue (residue number reindexed from 1): K44 L46 N47 K50 R55 H99 V176 R179 I358 G361 M362 R421 S513

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:5npk, PDBe:5npk, PDBj:5npk
• PDBsum: 5npk
• PubMed: 28507124
• UniProt: P66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
  Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)