3TU9 | pdb_00003tu9

Crystal structure of rabbit muscle aldolase bound with 5-O-methyl mannitol 1,6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb3TU9/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-09-16 Released: 2011-10-12 
• Deposition Author(s): Arthus-Cartier, G., Sygusch, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Mannitol Bis-phosphate Based Inhibitors of Fructose 1,6-Bisphosphate Aldolases.

Mabiala-Bassiloua, C.G., Arthus-Cartier, G., Hannaert, V., Therisod, H., Sygusch, J., Therisod, M.

(2011) ACS Med Chem Lett 2: 804-808

• PubMed: 24900268 
• DOI: https://doi.org/10.1021/ml200129s
• Primary Citation of Related Structures:  
  3TU9


• PubMed Abstract: 
  

  Several 5-O-alkyl- and 5-C-alkyl-mannitol bis-phosphates were synthesized and comparatively assayed as inhibitors of fructose bis-phosphate aldolases (Fbas) from rabbit muscle (taken as surrogate model of the human enzyme) and from Trypanosoma brucei. A limited selectivity was found in several instances. Crystallographic studies confirm that the 5-O-methyl derivative binds competitively with substrate and the 5-O-methyl moiety penetrating deeper into a shallow hydrophobic pocket at the active site. This observation can lead to the preparation of selective competitive or irreversible inhibitors of the parasite Fba.

---

Organizational Affiliation: 

ECBB, ICMMO (UMR 8182), LabEx LERMIT, Université Paris-Sud , UMR 8182, F-91405 Orsay, France.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 158.48 kDa 
• Atom Count: 12,270 
• Modelled Residue Count: 1,399 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase A	A, B, C, D	363	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: ALDOA EC: 4.1.2.13
UniProt
Find proteins for P00883 (Oryctolagus cuniculus) Explore P00883  Go to UniProtKB:  P00883

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5MM	E [auth A], F [auth B], G [auth C], H [auth D]	2-O-methyl-1,6-di-O-phosphono-D-mannitol C7 H18 O12 P2 QXWUAOXRWVSNDB-DBRKOABJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5MM	BindingDB:  3TU9	IC50: 7500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.669	α = 90
b = 103.056	β = 98.34
c = 84.458	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Arthus-Cartier, G., Sygusch, J.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description