4TIM

CRYSTALLOGRAPHIC AND MOLECULAR MODELING STUDIES ON TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE: A CRITICAL ASSESSMENT OF THE PREDICTED AND OBSERVED STRUCTURES OF THE COMPLEX WITH 2-PHOSPHOGLYCERATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallographic and molecular modeling studies on trypanosomal triosephosphate isomerase: a critical assessment of the predicted and observed structures of the complex with 2-phosphoglycerate.

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

(1991) J Med Chem 34: 2709-2718

  • DOI: 10.1021/jm00113a007
  • Primary Citation of Related Structures:  
    4TIM

  • PubMed Abstract: 
  • In the continuation of a project aimed at the rational design of drugs against diseases caused by trypanosomes, the crystal structure of trypanosomal triosephosphate isomerase in complex with the active site inhibitor 2-phosphoglycerate has been determined ...

    In the continuation of a project aimed at the rational design of drugs against diseases caused by trypanosomes, the crystal structure of trypanosomal triosephosphate isomerase in complex with the active site inhibitor 2-phosphoglycerate has been determined. Two alternative modeling protocols have been attempted to predict the mode of binding of this ligand. In the first protocol, certain key interactions were restrained in the modeling procedure. In the second protocol, a full search of ligand conformational space was performed. In both cases the protein scaffold was kept static. Both protocols produced models which were reasonably close to the observed structure (rms difference less than 2.0 A). Nevertheless, some essential features were missed by each of the protocols. The crystallographic structure of the 2-PGA TIM complex shows that the ligand binds fully within the active site of TIM, with partners for all but one of the ligand's strongly hydrogen bonding groups. Several of the interactions between the ligand and the active site of TIM are seen to be common to all of the complexes so far structurally characterized between trypanosomal triosephosphate isomerase and competitive inhibitors. Such key interactions appear to be the best guide in the prediction of the binding mode of a new inhibitor.


    Related Citations: 
    • The Adaptability of the Active Site of Trypanosomal Triosephosphate Isomerase as Observed in the Crystal Structures of Three Different Complexes
      Noble, M.E.M., Wierenga, R.K., Lambeir, A.-M., Opperdoes, F.R., Thunnissen, A.-M.W.H., Kalk, K.H., Groendijk, H., Hol, W.G.J.
      (1991) Proteins 10: 50
    • The Crystal Structure of the "Open" and the "Closed" Conformation of the Flexible Loop of Trypanosomal Triosephosphate Isomerase
      Wierenga, R.K., Noble, M.E.M., Postma, J.P.M., Groendijk, H., Kalk, K.H., Hol, W.G.J., Opperdoes, F.R.
      (1991) Proteins 10: 33
    • Refined 1.83 Angstroms Structure of Trypanosomal Triosephosphate Isomerase, Crystallized in the Presence of 2.4 M-Ammonium Sulphate. A Comparison with the Structure of the Trypanosomal Triosephosphate Isomerase-Glycerol-3-Phosphate Complex
      Wierenga, R.K., Noble, M.E.M., Vriend, G., Nauche, S., Hol, W.G.J.
      (1991) J Mol Biol 220: 995
    • Structure Determination of the Glycosomal Triosephosphate Isomerase from Trypanosoma Brucei Brucei at 2.4 Angstroms Resolution
      Wierenga, R.K., Kalk, K.H., Hol, W.G.J.
      (1987) J Mol Biol 198: 109
    • Preliminary Crystallographic Studies of Triosephosphate Isomerase from the Blood Parasite Trypanosoma Brucei Brucei
      Wierenga, R.K., Hol, W.G.J., Misset, O., Opperdoes, F.R.
      (1984) J Mol Biol 178: 487

    Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRIOSEPHOSPHATE ISOMERASEA, B250Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.3.1.1
UniProt
Find proteins for P04789 (Trypanosoma brucei brucei)
Explore P04789 
Go to UniProtKB:  P04789
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PG (Subject of Investigation/LOI)
Query on 2PG

Download Ideal Coordinates CCD File 
C [auth B]2-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
GXIURPTVHJPJLF-UWTATZPHSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2PG PDBBind:  4TIM Ki: 6.90e+6 (nM) from 1 assay(s)
Binding MOAD:  4TIM Ki: 6.90e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.59α = 90
b = 97.29β = 90
c = 46.7γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1992-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance