1B3N | pdb_00001b3n

BETA-KETOACYL CARRIER PROTEIN SYNTHASE AS A DRUG TARGET, IMPLICATIONS FROM THE CRYSTAL STRUCTURE OF A COMPLEX WITH THE INHIBITOR CERULENIN.

• PDB DOI: https://doi.org/10.2210/pdb1B3N/pdb

• Classification: CONDENSING ENZYMES
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-12-14 Released: 1999-04-06 
• Deposition Author(s): Moche, M., Schneider, G., Edwards, P., Dehesh, K., Lindqvist, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.270 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.186 (DCC) 

Literature

Structure of the complex between the antibiotic cerulenin and its target, beta-ketoacyl-acyl carrier protein synthase.

Moche, M., Schneider, G., Edwards, P., Dehesh, K., Lindqvist, Y.

(1999) J Biological Chem 274: 6031-6034

• PubMed: 10037680 
• DOI: https://doi.org/10.1074/jbc.274.10.6031
• Primary Citation Related Structures: 
  1B3N


• PubMed Abstract: 
  

  In the biosynthesis of fatty acids, the beta-ketoacyl-acyl carrier protein (ACP) synthases catalyze chain elongation by the addition of two-carbon units derived from malonyl-ACP to an acyl group bound to either ACP or CoA. The enzyme is a possible drug target for treatment of certain cancers and for tuberculosis. The crystal structure of the complex of the enzyme from Escherichia coli, and the fungal mycotoxin cerulenin reveals that the inhibitor is bound in a hydrophobic pocket formed at the dimer interface. Cerulenin is covalently attached to the active site cysteine through its C2 carbon atom. The fit of the inhibitor to the active site is not optimal, and there is thus room for improvement through structure based design.

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Organizational Affiliation: 
• Department of Medical Biochemistry and Biophysics, Doktorsringen 9A1, Karolinska Institutet, S-171 77 Stockholm, Sweden.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 43.18 kDa 
• Atom Count: 3,074 
• Modeled Residue Count: 411 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)	A	412	Escherichia coli K-12	Mutation(s): 0  Gene Names: FABF EC: 2.3.1.41 (PDB Primary Data), 2.3.1.179 (UniProt)
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
CER	B [auth A]	(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE C12 H19 N O3 QEPYZBPOTYDXNA-FECJWDPASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.270 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.186 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.394	α = 90
b = 76.394	β = 90
c = 147.675	γ = 120

Software Package:

Software Name	Purpose
SIGMAA	model building
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
SIGMAA	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-06 
Deposition Author(s): Moche, M., Schneider, G., Edwards, P., Dehesh, K., Lindqvist, Y.

Revision History  

• Version 1.0: 1999-04-06
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Structure summary