Structure of PDB 5bs3 Chain D Binding Site BS01

Receptor Information
>5bs3 Chain D (length=670) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEK
ARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHI
RTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEH
RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMRE
SFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARI
VGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAA
MRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLAN
GASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPT
AGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNK
ARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNN
LYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYN
LRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEK
QAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVR
DELTEIRDRFGDDRRTEIQL
Ligand information
>5bs3 Chain E (length=20) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agccgtagggccctacggct
....................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5bs3 Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2).
Resolution2.65 Å
Binding residue
(original residue number in PDB)		K460 L462 N463 K466 R471 H515 V626 R629 R1122 F1123 I1175 A1176 G1178 M1179 R1238 S1330
Binding residue
(residue number reindexed from 1)		K44 L46 N47 K50 R55 H99 V176 R179 R302 F303 I355 A356 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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5bs3, PDBe:5bs3, PDBj:5bs3
PDBsum5bs3
PubMed25851938
UniProtP0A0K8|GYRB_STAAU DNA gyrase subunit B (Gene Name=gyrB);
P20831

[Back to BioLiP]