3C56

Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(3-Hydroxypropyl)-glycolohydroxamic acid bisphosphate, a competitive inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3C56/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-30 Released: 2008-08-26 
• Deposition Author(s): Coincon, M., Sygusch, J., Potvin-Dulude, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.207 
• R-Value Work: 0.172 

Starting Model: experimental

Literature

Synthesis and Biochemical Evaluation of Selective Inhibitors of Class II Fructose Bisphosphate Aldolases: Towards New Synthetic Antibiotics.

Fonvielle, M., Coincon, M., Daher, R., Desbenoit, N., Kosieradzka, K., Barilone, N., Gicquel, B., Sygusch, J., Jackson, M., Therisod, M.

(2008) Chemistry 14: 8521-8529

• PubMed: 18688832 
• DOI: https://doi.org/10.1002/chem.200800857
• Primary Citation of Related Structures:  
  3C4U, 3C52, 3C56


• PubMed Abstract: 
  

  We report the synthesis and biochemical evaluation of selective inhibitors of class II (zinc-dependent) fructose bisphosphate aldolases. The most active compound is a simplified analogue of fructose bisphosphate, bearing a well-positioned metal chelating group. It is a powerful and highly selective competitive inhibitor of isolated class II aldolases. We report crystallographic studies of this inhibitor bound in the active site of the Helicobacter pylori enzyme. The compound also shows activity against Mycobacterium tuberculosis isolates.

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Organizational Affiliation: 

LCBB-ICMMO, UMR 8182, Université Paris-Sud, Orsay, France.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.35 kDa 
• Atom Count: 5,198 
• Modelled Residue Count: 591 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase	A, B	307	Helicobacter pylori	Mutation(s): 0  Gene Names: fba EC: 4.1.2.13
UniProt
Find proteins for P56109 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56109  Go to UniProtKB:  P56109

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PH4	D [auth A], F [auth B]	3-{hydroxy[(phosphonooxy)acetyl]amino}propyl dihydrogen phosphate C5 H13 N O10 P2 IISKWLQYGVRJHI-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PH4	PDBBind:  3C56	Ki: 13 (nM) from 1 assay(s)
	BindingDB:  3C56	Ki: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.207 
• R-Value Work: 0.172 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.222	α = 82.9
b = 62.005	β = 79.77
c = 65.615	γ = 71.03

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Coincon, M., Sygusch, J., Potvin-Dulude, P.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description