1A7K

GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A MONOCLINIC CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure.

Kim, H.Hol, W.G.

(1998) J Mol Biol 278: 5-11

  • DOI: 10.1006/jmbi.1998.1661
  • Primary Citation of Related Structures:  
    1A7K

  • PubMed Abstract: 
  • The structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the trypanosomatid parasite Leishmania mexicana in a new crystal form has been determined by X-ray crystallography. The protein crystallizes in space group P21 with one 156 kDa tetramer per asymmetric unit ...

    The structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the trypanosomatid parasite Leishmania mexicana in a new crystal form has been determined by X-ray crystallography. The protein crystallizes in space group P21 with one 156 kDa tetramer per asymmetric unit. The model of the protein with bound NAD+s and phosphates has been refined against 81% complete data from 10.0 to 2. 8 A to a crystallographic Rfactor of 0.217. The present structure confirms two key aspects of the previously reported orthorhombic crystal structure of L. mexicana GAPDH (LmGAPDH): the unusual conformation of a loop in the active site, and the repositioning of the inorganic phosphate binding site compared with crystal structures of GAPDHs from other organisms. As the monoclinic crystals of LmGAPDH were grown at a phosphate concentration and pH that were even closer to physiological conditions than were the orthorhombic LmGAPDH crystals, the present structure reinforces the physiological relevance of the active site structure seen in the previous orthorhombic crystal of LmGAPDH.


    Related Citations: 
    • Crystal Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Leishmania Mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site
      Kim, H., Feil, I.K., Verlinde, C.L., Petra, P.H., Hol, W.G.
      (1995) Biochemistry 34: 14975

    Organizational Affiliation

    Department of Biological Structure, Biomolecular Structure Center, Seattle, WA, 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASEA, B, C, D360Leishmania mexicanaMutation(s): 0 
Gene Names: GAPG
EC: 1.2.1.12
UniProt
Find proteins for Q27890 (Leishmania mexicana)
Explore Q27890 
Go to UniProtKB:  Q27890
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.9α = 90
b = 81β = 95
c = 131.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1998-03-16 
  • Released Date: 1998-06-17 
  • Deposition Author(s): Kim, H., Hol, W.G.J.

Revision History  (Full details and data files)

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance