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

Summary for 4TIM

• Entry DOI: 10.2210/pdb4tim/pdb
• Descriptor: TRIOSEPHOSPHATE ISOMERASE, 2-PHOSPHOGLYCERIC ACID (3 entities in total)
• Functional Keywords: isomerase(intramolecular oxidoreductase)
• Biological source: Trypanosoma brucei brucei
• Cellular location: Glycosome: P04789
• Total number of polymer chains: 2
• Total formula weight: 53917.72

Authors

Nobel, M.E.M.,Wierenga, R.K.,Hol, W.G.J. (deposition date: 1991-04-11, release date: 1992-10-15, Last modification date: 2024-02-28)

Primary citation

Noble, M.E.,Verlinde, C.L.,Groendijk, H.,Kalk, K.H.,Wierenga, R.K.,Hol, W.G.
Crystallographic and molecular modeling studies on trypanosomal triosephosphate isomerase: a critical assessment of the predicted and observed structures of the complex with 2-phosphoglycerate.
J.Med.Chem., 34:2709-2718, 1991

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. 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.

PubMed: 1895291
DOI: 10.1021/jm00113a007

Experimental method

X-RAY DIFFRACTION (2.4 Å)