3I8P

Crystal structure of E. coli FabF(C163A) in complex with Platensimycin A1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Isolation, enzyme-bound structure and antibacterial activity of platencin A1 from Streptomyces platensis.

Singh, S.B.Ondeyka, J.G.Herath, K.B.Zhang, C.Jayasuriya, H.Zink, D.L.Parthasarathy, G.Becker, J.W.Wang, J.Soisson, S.M.

(2009) Bioorg.Med.Chem.Lett. 19: 4756-4759

  • DOI: 10.1016/j.bmcl.2009.06.061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Natural products continue to serve as one of the best sources for discovery of antibacterial agents as exemplified by the recent discoveries of platensimycin and platencin. Chemical modifications as well as discovery of congeners are the main sources ...

    Natural products continue to serve as one of the best sources for discovery of antibacterial agents as exemplified by the recent discoveries of platensimycin and platencin. Chemical modifications as well as discovery of congeners are the main sources for gaining knowledge of structure-activity relationship of natural products. Screening for congeners in the extracts of the fermentation broths of Streptomyces platensis led to the isolation of platencin A(1), a hydroxy congener of platencin. The hydroxylation of the tricyclic enone moiety negatively affected the antibacterial activity and appears to be consistent with the hydrophobic binding pocket of the FabF. Isolation, structure, enzyme-bound structure and activity of platencin A(1) and two other congeners have been described.


    Organizational Affiliation

    Merck Research Laboratories, Rahway, NJ 07065, USA. sheo_singh@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-oxoacyl-[acyl-carrier-protein] synthase 2
A
427Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: fabF (fabJ)
EC: 2.3.1.179
Find proteins for P0AAI5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AAI5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
840
Query on 840

Download SDF File 
Download CCD File 
A
Platensimycin A1
2,4-dihydroxy-3-({3-[(1aR,2R,3R,3aS,7S,7aS,7bR)-3-hydroxy-2,7-dimethyl-6-oxo-2,3,7,7a-tetrahydro-6H-2,7b-epoxy-1a,3a-methanocyclopropa[a]naphthalen-7(1H)-yl]propanoyl}amino)benzoic acid
C24 H25 N O8
TUHIUIGYYSZKCN-ACYPNERUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
840IC50: 19 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.016α = 90.00
b = 76.016β = 90.00
c = 144.941γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
ADSCdata collection
MOLREPphasing
DENZOdata reduction
TNTrefinement
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description