2PGD

THE STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE REFINED AT 2 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2PGD/pdb
• Entry: 2PGD supersedes: 1PGD

• Classification: OXIDOREDUCTASE (CHOH(D)-NADP+(A))
• Organism(s): Ovis aries
• Mutation(s): No 


• Deposited: 1994-07-18 Released: 1995-02-27 
• Deposition Author(s): Adams, M.J., Phillips, C., Gover, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

The structure of 6-phosphogluconate dehydrogenase refined at 2.5 A resolution.

Adams, M.J., Gover, S., Leaback, R., Phillips, C., Somers, D.O.

(1991) Acta Crystallogr B 47: 817-820

• PubMed: 1793548 
• DOI: https://doi.org/10.1107/s0108768191010315
• Primary Citation of Related Structures:  
  2PGD


• PubMed Abstract: 
  

  The three-dimensional structure of ovine 6-phosphogluconate dehydrogenase, refined at 2.5 A resolution with a residual for all data of 18.5%, is reported. This model, based on improved diffraction data and a corrected sequence, supersedes that reported earlier. Each subunit of the dimer has three domains: a beta-alpha-beta domain binds NADP; an all alpha domain provides much of the dimer interface; the C-terminal tail burrows into the second subunit.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Oxford University, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 53.19 kDa 
• Atom Count: 4,015 
• Modelled Residue Count: 473 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-PHOSPHOGLUCONATE DEHYDROGENASE	A	482	Ovis aries	Mutation(s): 0  EC: 1.1.1.44
UniProt
Find proteins for P00349 (Ovis aries) Explore P00349  Go to UniProtKB:  P00349

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.74	α = 90
b = 148.4	β = 90
c = 102.35	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-02-27 
Deposition Author(s): Adams, M.J., Phillips, C., Gover, S.
• This entry supersedes: 1PGD

Revision History  

• 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: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations