Structure of PDB 5npk Chain B Binding Site BS01

Receptor Information
>5npk Chain B (length=673) Species: 158879 (Staphylococcus aureus subsp. aureus N315) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEK
ARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHI
RTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANNERNITSEM
RESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSA
RIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGA
AAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLL
ANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDF
PTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQV
NKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVIL
NNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQ
YNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLS
EKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQL
VRDELTEIRDRFGDDRRTEIQLG
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5npk Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		E435 G459 K460 D512 R1033 K1043 H1046 H1079 H1081 G1082 S1085 R1092 S1173 R1272
Binding residue
(residue number reindexed from 1)		E19 G43 K44 D96 R215 K225 H228 H261 H263 G264 S267 R274 S355 R454
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5npk, PDBe:5npk, PDBj:5npk
PDBsum5npk
PubMed28507124
UniProtP66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)

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