1A7K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.292 
  • R-Value Work: 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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
A, B, C, D
360Leishmania mexicanaGene Names: GAPG
EC: 1.2.1.12
Find proteins for Q27890 (Leishmania mexicana)
Go to UniProtKB:  Q27890
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.900α = 90.00
b = 81.000β = 95.00
c = 131.900γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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