Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 54.02 kDa 
• Atom Count: 3735 
• Residue Count: 471 
• Unique protein chains: 1

3ELC

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand

• DOI: 10.2210/pdb3ELC/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-09-22 Released: 2009-08-25 
• Deposition Author(s): Hunter, W.N., Ramsden, N.L., Ulaganathan, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.291 
• R-Value Work: 0.208 
• R-Value Observed: 0.213 

Literature

A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy

Ramsden, N.L., Buetow, L., Dawson, A., Kemp, L.A., Ulaganathan, V., Brenk, R., Klebe, G., Hunter, W.N.

(2009) J Med Chem 52: 2531-2542

• PubMed: 19320487 
• DOI: 10.1021/jm801475n
• Primary Citation of Related Structures:  
  3ELC, 3EOR, 3ERN, 3ESJ, 3FBA


• PubMed Abstract: 
  

The nonmevalonate route to isoprenoid biosynthesis is essential in Gram-negative bacteria and apicomplexan parasites. The enzymes of this pathway are absent from mammals, contributing to their appeal as chemotherapeutic targets. One enzyme, 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), has been validated as a target by genetic approaches in bacteria. Virtual screening against Escherichia coli IspF (EcIspF) was performed by combining a hierarchical filtering methodology with molecular docking. Docked compounds were inspected and 10 selected for experimental validation. A surface plasmon resonance assay was developed and two weak ligands identified. Crystal structures of EcIspF complexes were determined to support rational ligand development. Cytosine analogues and Zn(2+)-binding moieties were characterized. One of the putative Zn(2+)-binding compounds gave the lowest measured K(D) to date (1.92 +/- 0.18 muM). These data provide a framework for the development of IspF inhibitors to generate lead compounds of therapeutic potential against microbial pathogens.

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Organizational Affiliation: 

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A, B, C	165	Escherichia coli K-12	Mutation(s): 0  Gene Names: ispF, mecS, ygbB, b2746, JW2716 EC: 4.6.1.12
Find proteins for P62617 (Escherichia coli (strain K12)) Explore P62617  Go to UniProtKB:  P62617

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GPP	C	GERANYL DIPHOSPHATE C10 H20 O7 P2 GVVPGTZRZFNKDS-JXMROGBWSA-N
F01	A, B, C	4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-fluoro-pyrimidin-2-one C9 H12 F N3 O5 STRZQWQNZQMHQR-UAKXSSHOSA-N
ZN	A, B, C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
F01	Kd:  2020000   nM  Binding MOAD
F01	Kd:  2020000   nM  BindingDB
F01	Kd :  2020000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.291 
• R-Value Work: 0.208 
• R-Value Observed: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.676	α = 90
b = 54.833	β = 99.66
c = 88.506	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-22 
• Released Date: 2009-08-25 
Deposition Author(s): Hunter, W.N., Ramsden, N.L., Ulaganathan, V.

Revision History 

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description