1MZS | pdb_00001mzs

CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III WITH BOUND dichlorobenzyloxy-indole-carboxylic acid inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1MZS/pdb

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


• Deposited: 2002-10-09 Released: 2002-11-13 
• Deposition Author(s): Daines, R.A., Pendrak, I., Sham, K., Van Aller, G.S., Konstantinidis, A.K., Lonsdale, J.T., Janson, C.A., Qui, X., Brandt, M., Silverman, C., Head, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

First X-ray cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor achieved using rational design and homology modeling

Daines, R.A., Pendrak, I., Sham, K., Van Aller, G.S., Konstantinidis, A.K., Lonsdale, J.T., Janson, C.A., Qiu, X., Brandt, M., Khandekar, S.S., Silverman, C., Head, M.S.

(2003) J Med Chem 46: 5-8

• PubMed: 12502353 
• DOI: https://doi.org/10.1021/jm025571b
• Primary Citation Related Structures: 
  1MZS


• PubMed Abstract: 
  

  The first cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor is reported. The inhibitor was obtained by rational modification of a high throughput screening lead with the aid of a S. pneumoniae FabH homology model. This homology model was used to design analogues that would have both high affinity for the enzyme and appropriate aqueous solubility to facilitate cocrystallization studies.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 34.14 kDa 
• Atom Count: 2,559 
• Modeled Residue Count: 317 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase III	A	317	Escherichia coli	Mutation(s): 1  EC: 2.3.1.41 (PDB Primary Data), 2.3.1.180 (UniProt)
UniProt
Find proteins for P0A6R0 (Escherichia coli (strain K12)) Explore P0A6R0  Go to UniProtKB:  P0A6R0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
669	C [auth A]	1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID C22 H21 Cl2 N O5 JTGPYFFQVOIJKR-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.34	α = 90
b = 72.34	β = 90
c = 100.73	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
X-PLOR	model building
CNS	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-13 
Deposition Author(s): Daines, R.A., Pendrak, I., Sham, K., Van Aller, G.S., Konstantinidis, A.K., Lonsdale, J.T., Janson, C.A., Qui, X., Brandt, M., Silverman, C., Head, M.S.

Revision History  

• Version 1.0: 2002-11-13
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary