1AG1 | pdb_00001ag1

MONOHYDROGEN PHOSPHATE BINDING TO TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE

• PDB DOI: https://doi.org/10.2210/pdb1AG1/pdb

• Classification: ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
• Organism(s): Trypanosoma brucei
• Mutation(s): No 


• Deposited: 1997-03-28 Released: 1997-06-16 
• Deposition Author(s): Verlinde, C.L.M.J., Hol, W.G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Work: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Anion binding at the active site of trypanosomal triosephosphate isomerase. Monohydrogen phosphate does not mimic sulphate.

Verlinde, C.L., Noble, M.E., Kalk, K.H., Groendijk, H., Wierenga, R.K., Hol, W.G.

(1991) Eur J Biochem 198: 53-57

• PubMed: 2040290 
• DOI: https://doi.org/10.1111/j.1432-1033.1991.tb15985.x
• Primary Citation Related Structures: 
  1AG1


• PubMed Abstract: 
  

  The three-dimensional structure of triosephosphate isomerase complexed with the competitive inhibitor SO-4(2) was determined by X-ray crystallography to a resolution of 0.24 nm. A comparison with the native crystal structure, where SO-4(2) is bound, revealed five changes: (a) a 0.10-nm shift of the anion-binding site; (b) a further closing of the flexible loop of the enzyme; (c) a 'swinging in' of the side chain of the catalytic Glu, that is chi 1 changes from (+) to (-) synclinal; (d) an altered water structure; (e) a disappearance of the conformational heterogeneity at the C-terminus of strand beta 7. Some of these changes may be related to the different hydrogen-bond pattern about the two different anions. However, the distance of 0.10 nm between the sulphur and phosphorus positions is unexpected and remains intriguing.

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Organizational Affiliation: 
• BIOSON Research Institute, University of Groningen, The Netherlands.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 53.83 kDa 
• Atom Count: 3,927 
• Modeled Residue Count: 498 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIOSEPHOSPHATE ISOMERASE	A [auth O], B [auth T]	250	Trypanosoma brucei	Mutation(s): 0  EC: 5.3.1.1
UniProt
Find proteins for P04789 (Trypanosoma brucei brucei) Explore P04789  Go to UniProtKB:  P04789

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth T]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Work:  0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.84	α = 90
b = 97.6	β = 90
c = 46.7	γ = 90

Software Package:

Software Name	Purpose
ISOMORPHOUS	model building
TNT	refinement
MADNES	data reduction
BIOMOL	data scaling
ISOMORPHOUS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-06-16 
Deposition Author(s): Verlinde, C.L.M.J., Hol, W.G.J.

Revision History  

• Version 1.0: 1997-06-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-18
  Changes: Data collection, Other
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection