6QTP

2.37A structure of gepotidacin with S.aureus DNA gyrase and uncleaved DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanistic and Structural Basis for the Actions of the Antibacterial Gepotidacin against Staphylococcus aureus Gyrase.

Gibson, E.G.Bax, B.Chan, P.F.Osheroff, N.

(2019) ACS Infect Dis --: --


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)Mutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P66937
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, C
490Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: gyrA
EC: 5.6.2.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*AP*GP*CP*TP*GP*TP*AP*CP*GP*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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B
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
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
JHN
Query on JHN

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E
(3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione
C24 H28 N6 O3
PZFAZQUREQIODZ-LJQANCHMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.341α = 90.00
b = 123.653β = 117.10
c = 94.099γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-02-25 
  • Released Date: 2019-03-13 
  • Deposition Author(s): Bax, B.D.

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release