6SZH

Acinetobacter baumannii undecaprenyl pyrophosphate synthase (AB-UppS) in complex with GW197


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Cocktailed fragment screening by X-ray crystallography of the antibacterial target undecaprenyl pyrophosphate synthase from Acinetobacter baumannii.

Thorpe, J.H.Wall, I.D.Sinnamon, R.H.Taylor, A.N.Stavenger, R.A.

(2020) Acta Crystallogr F Struct Biol Commun 76: 40-46

  • DOI: https://doi.org/10.1107/S2053230X19017199
  • Primary Citation of Related Structures:  
    6SZG, 6SZH

  • PubMed Abstract: 

    Direct soaking of protein crystals with small-molecule fragments grouped into complementary clusters is a useful technique when assessing the potential of a new crystal system to support structure-guided drug discovery. It provides a robustness check prior to any extensive crystal screening, a double check for assay binding cutoffs and structural data for binding pockets that may or may not be picked out in assay measurements. The structural output from this technique for three novel fragment molecules identified to bind to the antibacterial target Acinetobacter baumannii undecaprenyl pyrophosphate synthase are reported, and the different physicochemical requirements of a successful antibiotic are compared with traditional medicines.


  • Organizational Affiliation

    GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
A, B
270Acinetobacter baumanniiMutation(s): 0 
Gene Names: 
EC: 2.5.1.31
UniProt
Find proteins for V5VCK8 (Acinetobacter baumannii)
Explore V5VCK8 
Go to UniProtKB:  V5VCK8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5VCK8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.3α = 90
b = 64.12β = 92.7
c = 71.6γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-01-22 
  • Deposition Author(s): Thorpe, J.H.

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description