5NPK

1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.154

Literature

Macromolecules
Sequence Display for 5NPK

Classification: ISOMERASE

Total Structure Weight: 341501.88


Macromolecule Entities
Molecule Chains Length Organism Details
DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit A B, D, b, d 692 Staphylococcus aureus EC#: 5.99.1.3 IUBMB
Mutation: Y1123F
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, e, f 20 Synthetic construct

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
94H
Query on 94H

B, D, b, d ~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-4- (1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene- 2-carboxamide
C20 H18 N4 O S
ZNBOMXQVNVLXCZ-KRWDZBQOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
9JN
Query on 9JN

b, e ~{N}-[(1~{S})-2-azanyl-1-phenyl-ethyl]-4- (1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene- 2-carboxamide
C20 H18 N4 O S
ZNBOMXQVNVLXCZ-QGZVFWFLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

b SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B, D, b, d, e GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

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

D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 1.98 Å
  • R-Value Free: 0.183
  • R-Value Work: 0.154
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 89.44 α = 90.00
b = 120.68 β = 90.05
c = 168.90 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-04-17
  • Released Date: 2017-07-12
  • Deposition author(s): Bax, B.D., Chan, P.F., Stavenger, R.A.

Revision History

  • 2017-08-23
    Type: Advisory