1IF2

X-RAY STRUCTURE OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE COMPLEXED WITH IPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural determinants for ligand binding and catalysis of triosephosphate isomerase.

Kursula, I.Partanen, S.Lambeir, A.M.Antonov, D.M.Augustyns, K.Wierenga, R.K.

(2001) Eur.J.Biochem. 268: 5189-5196


  • PubMed Abstract: 
  • The crystal structure of leishmania triosephosphate isomerase (TIM) complexed with 2-(N-formyl-N-hydroxy)-aminoethyl phosphonate (IPP) highlights the importance of Asn11 for binding and catalysis. IPP is an analogue of the substrate D-glyceraldehyde- ...

    The crystal structure of leishmania triosephosphate isomerase (TIM) complexed with 2-(N-formyl-N-hydroxy)-aminoethyl phosphonate (IPP) highlights the importance of Asn11 for binding and catalysis. IPP is an analogue of the substrate D-glyceraldehyde-3-phosphate, and it is observed to bind with its aldehyde oxygen in an oxyanion hole formed by ND2 of Asn11 and NE2 of His95. Comparison of the mode of binding of IPP and the transition state analogue phosphoglycolohydroxamate (PGH) suggests that the Glu167 side chain, as well as the triose part of the substrate, adopt different conformations as the catalysed reaction proceeds. Comparison of the TIM-IPP and the TIM-PGH structures with other liganded and unliganded structures also highlights the conformational flexibility of the ligand and the active site, as well as the conserved mode of ligand binding.


    Organizational Affiliation

    Biocenter Oulu and Department of Biochemistry, University of Oulu, FIN-90014, Oulu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE
A
251Leishmania mexicanaEC: 5.3.1.1
Find proteins for P48499 (Leishmania mexicana)
Go to UniProtKB:  P48499
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
129
Query on 129

Download SDF File 
Download CCD File 
A
[2(FORMYL-HYDROXY-AMINO)-ETHYL]-PHOSPHONIC ACID
C3 H8 N O5 P
NBAIGNUEKZLOMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.234α = 90.00
b = 52.825β = 118.03
c = 58.937γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance