6FQS

3.11A complex of S.Aureus gyrase with imidazopyrazinone T3 and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance.

Germe, T.Voros, J.Jeannot, F.Taillier, T.Stavenger, R.A.Bacque, E.Maxwell, A.Bax, B.D.

(2018) Nucleic Acids Res. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B,DNA gyrase subunit B
B, D
202Staphylococcus aureus (strain N315)Gene Names: gyrB
EC: 5.99.1.3
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P66937
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A
490Staphylococcus aureus (strain N315)Gene Names: gyrA
EC: 5.99.1.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
C
490Staphylococcus aureus (strain N315)Gene Names: gyrA
EC: 5.99.1.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*TP*T)-3')E,F20synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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B, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, C, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
E3E
Query on E3E

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E
5-cyclopropyl-8-fluoranyl-7-pyridin-4-yl-imidazo[1,2-a]quinoxalin-4-one
C18 H13 F N4 O
UZAPAHIWOLYIFO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
C
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 94.027α = 90.00
b = 94.027β = 90.00
c = 420.470γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Innovative Medicines Initiative Joint Undertaking115583

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release