Brand  (β version)

PDB ID: 6QX2

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Ligands
Code Name Style Show Link
JK8 (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine PoSSuM
Non-standard Residues
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Glycosylation
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Structure summary

Code : 6QX2   PDBj   RCSB PDB   PDBe
Header : ISOMERASE
Title : 3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA
Release Data : 2019-04-17
Compound :
mol_id molecule chains
1 DNA gyrase subunit B,DNA gyrase subunit B B,S,b,s
ec: 5.99.1.3,5.99.1.3
mol_id molecule chains
2 DNA gyrase subunit A A,C,L,R,T,a,c,j,l,r,t
ec: 5.99.1.3
mutation: 123 phosphotyrosine
mol_id molecule chains
3 DNA gyrase subunit B,DNA gyrase subunit B D,U,m
ec: 5.99.1.3,5.99.1.3
mol_id molecule chains
4 DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') E,F,N,O,W,e,n,v,w
mol_id molecule chains
5 DNA gyrase subunit B,DNA gyrase subunit B K
ec: 5.99.1.3,5.99.1.3
mol_id molecule chains
6 DNA gyrase subunit A J
ec: 5.99.1.3
mol_id molecule chains
7 DNA gyrase subunit B,DNA gyrase subunit B M
ec: 5.99.1.3,5.99.1.3
mol_id molecule chains
8 DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') V,o
mol_id molecule chains
9 DNA gyrase subunit B,DNA gyrase subunit B d
ec: 5.99.1.3,5.99.1.3
mol_id molecule chains
10 DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') f
mol_id molecule chains
11 DNA gyrase subunit B,DNA gyrase subunit B k
ec: 5.99.1.3,5.99.1.3
mol_id molecule chains
12 DNA gyrase subunit B,DNA gyrase subunit B u
ec: 5.99.1.3,5.99.1.3
Source :
mol_id organism_scientific expression_system
1 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrB, SAV0005
mol_id organism_scientific expression_system
2 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrA, SA0006
mol_id organism_scientific expression_system
3 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrB, SAR0005
mol_id organism_scientific expression_system
4 Synthetic construct  (taxid:32630) Synthetic construct  (taxid:32630)
mol_id organism_scientific expression_system
5 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrB, SAUSA300_0005
mol_id organism_scientific expression_system
6 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrA, SA0006
mol_id organism_scientific expression_system
7 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrB, SAUSA300_0005
mol_id organism_scientific expression_system
8 Synthetic construct  (taxid:32630) Synthetic construct  (taxid:32630)
mol_id organism_scientific expression_system
9 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrB, SAR0005
mol_id organism_scientific expression_system
10 Synthetic construct  (taxid:32630) Synthetic construct  (taxid:32630)
mol_id organism_scientific expression_system
11 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrB, SAR0005
mol_id organism_scientific expression_system
12 Staphylococcus aureus  (taxid:1280) Escherichia coli  (taxid:562)
gene: gyrB, SAUSA300_0005
Authors : Bax, B.D.
Keywords : Inhibitor, DNA complex, isomerase
Exp. method : X-RAY DIFFRACTION ( 3.40 Å )
Citation :

Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.

Thalji, R.K.,Raha, K.,Andreotti, D.  et al.
(2019)  Bioorg.Med.Chem.Lett.  29 : 1407 - 1412

PubMed: 30962087
DOI: 10.1016/j.bmcl.2019.03.029

Reaction

Chain : D, U, m
UniProt : P0A0K8 (GYRB_STAAU)
Reaction: EC: Evidence:
Physiological Direction:
ATP-dependent breakage, passage and rejoining of double- stranded DNA. 5.6.2.2 HAMAP-Rule:MF_01898
-
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, S, b, s
UniProt : P66936 (GYRB_STAAM)
Reaction: EC: Evidence:
Physiological Direction:
ATP-dependent breakage, passage and rejoining of double- stranded DNA. 5.6.2.2 HAMAP-Rule:MF_01898
-
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 : J
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
-
Chain : k
UniProt : Q6GKU0 (GYRB_STAAR)
Reaction: EC: Evidence:
Physiological Direction:
ATP-dependent breakage, passage and rejoining of double- stranded DNA. 5.6.2.2 HAMAP-Rule:MF_01898
-
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 : u
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
-
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 : u
UniProt : Q2FKQ1 (GYRB_STAA3)
Reaction: EC: Evidence:
Physiological Direction:
ATP-dependent breakage, passage and rejoining of double- stranded DNA. 5.6.2.2 HAMAP-Rule:MF_01898
-
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+).