5NPP

2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYRASE AND DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.182

Literature

Macromolecules
Sequence Display for 5NPP

Classification: ISOMERASE

Total Structure Weight: 170663.14


Macromolecule Entities
Molecule Chains Length Organism Details
DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A B, D 692 Staphylococcus aureus EC#: 5.99.1.3 IUBMB
Gene Name(s): gyrB SA0005 gyrA SA0006
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
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 8 Synthetic construct
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 12 Synthetic construct

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
6EJ
Query on 6EJ

C (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
C24 H26 F N5 O3
SRICOHRDRMZREQ-MRXNPFEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
94K
Query on 94K

B, D ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5- (2-chlorophenyl)-2-methyl-thiophene-3-carboxamide
C20 H19 Cl N2 O S
GEDDMFGBKRREEU-SFHVURJKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

B DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

B, D MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.182
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 92.85 α = 90.00
b = 92.85 β = 90.00
c = 409.98 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-18
  • Released Date: 2017-07-12
  • Deposition author(s): Bax, B.D., Chan, P.F., Stavenger, R.A.

Revision History

  • Version 1_0: 2017-07-12

    Type: Initial release