1SZJ

STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM PALINURUS VERSICOLOR REFINED 2.0 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Preliminary crystallographic studies of lobster D-glyceraldehyde-3-phosphate dehydrogenase and the modified enzyme carrying the fluorescent derivative.

Song, S.Y.Gao, Y.G.Zhou, J.M.Tsou, C.L.

(1983) J.Mol.Biol. 171: 225-228


  • PubMed Abstract: 
  • When the active-site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase is irradiated with ultraviolet light in the presence of NAD+, a fluorescent NAD derivative that is covalently linked to the enzyme is obtained. A preliminary crystallog ...

    When the active-site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase is irradiated with ultraviolet light in the presence of NAD+, a fluorescent NAD derivative that is covalently linked to the enzyme is obtained. A preliminary crystallographic study of this fluorescent derivative, as well as of the native and the carboxymethylated enzymes from Palinurus versicolor, showed that they are isomorphous and belong to space group C2 as reported for the native enzyme from Palinurus vulgaris. The three forms of the enzyme, although they have identical unit cell parameters, differ considerably in their diffraction patterns, indicating marked differences in conformation in spite of the fact that they differ chemically only in a restricted region around the active site.


    Related Citations: 
    • Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase from Palinurus Versicolor Carrying the Fluorescent Nad Derivatives at 2.7 A Resolution
      Lin, Z.J.,Li, J.,Zhang, F.M.,Song, S.Y.,Yang, J.,Liang, S.J.,Tsou, C.L.
      (1993) Arch.Biochem.Biophys. 302: 161



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
G, R
333Panulirus versicolorMutation(s): 0 
EC: 1.2.1.12
Find proteins for P56649 (Panulirus versicolor)
Go to UniProtKB:  P56649
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
G, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
G, R
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.400α = 90.00
b = 99.900β = 114.48
c = 80.790γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-02-04 
  • Released Date: 1998-09-16 
  • Deposition Author(s): Song, S., Li, J., Lin, Z.

Revision History 

  • Version 1.0: 1998-09-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance