3G0Y | pdb_00003g0y

Structure of E. coli FabF(C163Q) in complex with dihydroplatensimycin

• PDB DOI: https://doi.org/10.2210/pdb3G0Y/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-01-29 Released: 2009-03-17 
• Deposition Author(s): Soisson, S.M., Parthasarathy, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.234 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Synthesis and biological evaluation of platensimycin analogs.

Shen, H.C., Ding, F.X., Singh, S.B., Parthasarathy, G., Soisson, S.M., Ha, S.N., Chen, X., Kodali, S., Wang, J., Dorso, K., Tata, J.R., Hammond, M.L., Maccoss, M., Colletti, S.L.

(2009) Bioorg Med Chem Lett 19: 1623-1627

• PubMed: 19233644 
• DOI: https://doi.org/10.1016/j.bmcl.2009.02.006
• Primary Citation Related Structures: 
  3G0Y, 3G11


• PubMed Abstract: 
  

  Platensimycin (1) displays antibacterial activity due to its inhibition of the elongation condensing enzyme (FabF), a novel mode of action that could potentially lead to a breakthrough in developing a new generation of antibiotics. The medicinal chemistry efforts were focused on the modification of the enone moiety of platensimycin and several analogs showed significant activity against FabF and possess antibacterial activity.

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Organizational Affiliation: 
• Departments of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065-0900, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.11 kDa 
• Atom Count: 3,223 
• Modeled Residue Count: 411 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 2	A	427	Escherichia coli K-12	Mutation(s): 1  Gene Names: b1095, fabF, fabJ, JW1081 EC: 2.3.1.179
UniProt
Find proteins for P0AAI5 (Escherichia coli (strain K12)) Explore P0AAI5  Go to UniProtKB:  P0AAI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P9A	B [auth A]	3-({3-[(1S,4aS,6S,7S,9S,9aR)-1,6-dimethyl-2-oxodecahydro-6,9-epoxy-4a,7-methanobenzo[7]annulen-1-yl]propanoyl}amino)-2,4-dihydroxybenzoic acid C24 H29 N O7 XADCWKSMHQPTGH-OFBLZTNGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.234 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.032	α = 90
b = 76.032	β = 90
c = 147.041	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Soisson, S.M., Parthasarathy, G.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 2.0: 2021-10-20
  Changes: Atomic model, Database references, Derived calculations
• Version 2.1: 2023-09-06
  Changes: Data collection, Refinement description