1PGP

CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism.

Adams, M.J.Ellis, G.H.Gover, S.Naylor, C.E.Phillips, C.

(1994) Structure 2: 651-668

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidative decarboxylase, 6-phosphogluconate dehydrogenase, is a major source of reduced coenzyme for synthesis. Enzymes later in the pentose phosphate pathway convert the reaction produ ...

    The nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidative decarboxylase, 6-phosphogluconate dehydrogenase, is a major source of reduced coenzyme for synthesis. Enzymes later in the pentose phosphate pathway convert the reaction product, ribulose 5-phosphate, to ribose 5-phosphate. Crystallographic study of complexes with coenzyme and substrate explain the NADP dependence which determines the enzyme's metabolic role and support the proposed general base-general acid mechanism.


    Related Citations: 
    • The Structure of 6-Phosphogluconate Dehydrogenase Refined at 2 Angstroms Resolution
      Phillips, C.,Gover, S.,Adams, M.J.
      () TO BE PUBLISHED --: --
    • The Structure of 6-Phosphogluconate Dehydrogenase Refined at 2.5 Angstroms Resolution
      Adams, M.J.,Gover, S.,Leaback, R.,Phillips, C.,Somers, D.O'N.
      (1991) Acta Crystallogr.,Sect.B 47: 817


    Organizational Affiliation

    University of Oxford, Laboratory of Molecular Biophysics, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-PHOSPHOGLUCONATE DEHYDROGENASE
A
482Ovis ariesMutation(s): 0 
Gene Names: PGD
EC: 1.1.1.44
Find proteins for P00349 (Ovis aries)
Go to Gene View: PGD
Go to UniProtKB:  P00349
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
6PG
Query on 6PG

Download SDF File 
Download CCD File 
A
6-PHOSPHOGLUCONIC ACID
C6 H13 O10 P
BIRSGZKFKXLSJQ-SQOUGZDYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6PGKd: 2000 nM BINDINGMOAD
6PGKd: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 72.740α = 90.00
b = 148.400β = 90.00
c = 102.350γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-27
    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
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other