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: 2.50 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


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

  • DOI: 10.1016/s0969-2126(00)00066-6
  • Primary Citation of Related Structures:  
    1PGN, 1PGO, 1PGP, 1PGQ

  • 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 product, ribulose 5-phosphate, to ribose 5-phosphate ...

    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 B 47: 817

    Organizational Affiliation

    University of Oxford, Laboratory of Molecular Biophysics, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-PHOSPHOGLUCONATE DEHYDROGENASEA482Ovis ariesMutation(s): 0 
Gene Names: PGD
EC: 1.1.1.44
UniProt
Find proteins for P00349 (Ovis aries)
Explore P00349 
Go to UniProtKB:  P00349
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6PG (Subject of Investigation/LOI)
Query on 6PG

Download Ideal Coordinates CCD File 
B [auth A]6-PHOSPHOGLUCONIC ACID
C6 H13 O10 P
BIRSGZKFKXLSJQ-SQOUGZDYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6PG BindingDB:  1PGP Kd: 1995 (nM) from 1 assay(s)
Binding MOAD:  1PGP Kd: 2000 (nM) from 1 assay(s)
PDBBind:  1PGP Kd: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.74α = 90
b = 148.4β = 90
c = 102.35γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other