Brand  (β version)

PDB ID: 5NPP

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
6EJ (1r)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-C]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4h-pyrrolo[3,2,1-ij]quinolin-4-one PoSSuM
94K ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide PoSSuM
DMS Dimethyl sulfoxide PoSSuM
GOL Glycerol PoSSuM
MN Manganese (II) ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 5NPP   PDBj   RCSB PDB   PDBe
Header : ISOMERASE
Title : 2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 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
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
mol_id molecule chains
3 DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') A,C
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
2 synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 synthetic construct  (taxid:32630)
synthetic: yes
Authors : Bax, B.D., Chan, P.F., Stavenger, R.A.
Keywords : TYPE IIA TOPOISOMERASE, ANTIBACTERIAL, INHIBITOR, ISOMERASE
Exp. method : X-RAY DIFFRACTION ( 2.2200 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
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
-
Chain : 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
-