1J0X

Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of rabbit-muscle glyceraldehyde-3-phosphate dehydrogenase.

Cowan-Jacob, S.W.Kaufmann, M.Anselmo, A.N.Stark, W.Grutter, M.G.

(2003) Acta Crystallogr D Biol Crystallogr 59: 2218-2227

  • DOI: 10.1107/s0907444903020493
  • Primary Citation of Related Structures:  
    1J0X

  • PubMed Abstract: 
  • The crystal structure of the tetrameric form of D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) isolated from rabbit muscle was solved at 2.4 A resolution after careful dynamic light-scattering experiments to find a suitable buffer for crystallization trials ...

    The crystal structure of the tetrameric form of D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) isolated from rabbit muscle was solved at 2.4 A resolution after careful dynamic light-scattering experiments to find a suitable buffer for crystallization trials. The refined model has a crystallographic R factor of 20.3%. Here, the first detailed model of a mammalian GAPDH is presented. The cofactor NAD(+) (nicotinamide adenine dinucleotide) is bound to two subunits of the tetrameric enzyme, which is consistent with the negative cooperativity of NAD(+) binding to this enzyme. The structure of rabbit-muscle GAPDH is of interest because it shares 91% sequence identity with the human enzyme; human GAPDH is a potential target for the development of anti-apoptotic drugs. In addition, differences in the cofactor-binding pocket compared with the homology-model structure of GAPDH from the malaria parasite Plasmodium falciparum could be exploited in order to develop novel selective and potential antimalaria drugs.


    Organizational Affiliation

    Novartis Pharma AG, Core Technology Area, Analytics and Biomolecular Structure, CH-4002 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glyceraldehyde-3-phosphate dehydrogenase OPQR332Oryctolagus cuniculusMutation(s): 1 
Gene Names: GAPDHGAPD
EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (UniProt)
Find proteins for P46406 (Oryctolagus cuniculus)
Explore P46406 
Go to UniProtKB:  P46406
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
P, R
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
O,P,Q,RL-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NADKd:  10   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.7α = 90
b = 98.5β = 90
c = 183.1γ = 90
Software Package:
Software NamePurpose
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description