Brand  (β version)

PDB ID: 5NPK

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Ligands
Code Name Style Show Link
MN Manganese (II) ion PoSSuM
94H ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-B]pyridin-3-yl)thiophene-2-carboxamide PoSSuM
GOL Glycerol PoSSuM
CL Chloride ion PoSSuM
Non-standard Residues
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Glycosylation
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Structure summary

Code : 5NPK   PDBj   RCSB PDB   PDBe
Header : ISOMERASE
Title : 1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA
Release Data : 2017-07-12
Compound :
mol_id molecule chains
1 DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A B,D,b,d
ec: 5.99.1.3,5.99.1.3,5.99.1.3
mol_id molecule chains
2 DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') E,F,e,f
Source :
mol_id organism_scientific expression_system
1 Staphylococcus aureus  (taxid:158879) Escherichia coli  (taxid:562)
strain: N315
gene: gyrA, SA0006
mol_id organism_scientific expression_system
2 Synthetic construct  (taxid:32630) Synthetic construct  (taxid:32630)
Authors : Bax, B.D., Chan, P.F., Stavenger, R.A.
Keywords : TYPE IIA TOPOISOMERASE, ANTIBACTERIAL, INHIBITOR, ISOMERASE
Exp. method : X-RAY DIFFRACTION ( 1.9800 Å )
Citation :

Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.

Chan, P.F.,Germe, T.,Bax, B.D.  et al.
(2017)  Proc. Natl. Acad. Sci. U.S.A.  114 : E4492 - E4500

PubMed: 28507124
DOI: 10.1073/pnas.1700721114

Reaction

Chain : B, D, b, d
UniProt : P66937 (GYRB_STAAN)
Reaction: EC: Evidence:
Physiological Direction:
ATP-dependent breakage, passage and rejoining of double- stranded DNA. 5.6.2.2 HAMAP-Rule:MF_01898
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Cofactor: Evidence: Note:
Ca(2+) ECO:0000255 | HAMAP-Rule:MF_01898
ECO:0000255 | HAMAP-Rule:MF_01898
ECO:0000255 | HAMAP-Rule:MF_01898
Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+).
Chain : B, D, b, d
UniProt : Q99XG5 (GYRA_STAAN)
Reaction: EC: Evidence:
Physiological Direction:
ATP-dependent breakage, passage and rejoining of double- stranded DNA. 5.6.2.2 HAMAP-Rule:MF_01897
-