Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 60.34 kDa 
• Atom Count: 4572 
• Modelled Residue Count: 514 
• Deposited Residue Count: 534 
• Unique protein chains: 1

1PE1

Aquifex aeolicus KDO8PS in complex with cadmium and 2-PGA

• DOI: 10.2210/pdb1PE1/pdb

• Classification: LYASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-05-20 Released: 2004-02-03 
• Deposition Author(s): Wang, J., Xu, X., Grison, C., Petek, S., Coutrot, P., Birck, M.R., Woodard, R.W., Gatti, D.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.237 
• R-Value Work: 0.193 

Literature

Structure-Based Design of Novel Inhibitors of 3-Deoxy-D-manno-octulosonate 8-Phosphate Synthase

Xu, X., Wang, J., Grison, C., Petek, S., Coutrot, P., Birck, M.R., Woodard, R.W., Gatti, D.L.

(2003) Drug Des Discov 18: 91-99

• PubMed: 14675946 
• Primary Citation of Related Structures:  
  1PCK, 1PCW, 1PE1


• PubMed Abstract: 
  

3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) is the phosphorylated precursor of KDO, an essential sugar of the lipopolysaccharide of Gram negative bacteria. KDO8P is produced by a specific synthase (KDO8PS) by condensing arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP), with release of inorganic phosphate. As KDO8PS is present in bacteria and plants, but not in mammalian cells, and mutations that inactivate KDO8PS also block cell replication, KDO8PS is a promising target for the design of new antimicrobials that act by blocking lipopolysaccharide biosynthesis. Previous studies have shown that a compound mimicking an intermediate of the condensation reaction is a good ligand and a powerful inhibitor. Here we report on the crystallographic investigation of the binding to KDO8PS of new derivatives of this original inhibitor. The structures of the enzyme in complex with these compounds, and also with the PEP analogs, 2-phosphoglyceric acid (2-PGA) and Z-methyl-PEP, point to future strategies for the design of novel inhibitors of KDO8PS.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, 48201 USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A, B	267	Aquifex aeolicus	Mutation(s): 0  Gene Names: kdsA EC: 4.1.2.16 (PDB Primary Data), 2.5.1.55 (UniProt)
UniProt
Find proteins for O66496 (Aquifex aeolicus (strain VF5)) Explore O66496  Go to UniProtKB:  O66496

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PG (Subject of Investigation/LOI)	E [auth A], H [auth B]	2-PHOSPHOGLYCERIC ACID C3 H7 O7 P GXIURPTVHJPJLF-UWTATZPHSA-N
CD	D [auth A], G [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.237 
• R-Value Work: 0.193 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.434	α = 90
b = 84.434	β = 90
c = 159.751	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2003-05-20 
• Released Date: 2004-02-03 
Deposition Author(s): Wang, J., Xu, X., Grison, C., Petek, S., Coutrot, P., Birck, M.R., Woodard, R.W., Gatti, D.L.

Revision History  

• Version 1.0: 2004-02-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model