Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 55.00 kDa 
• Atom Count: 3920 
• Modelled Residue Count: 476 
• Deposited Residue Count: 497 
• Unique protein chains: 1

2P4Q

Crystal Structure Analysis of Gnd1 in Saccharomyces cerevisiae

• PDB DOI: 10.2210/pdb2P4Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-12 Released: 2007-07-24 
• Deposition Author(s): He, W., Wang, Y., Liu, W., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.220 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Literature

Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate dehydrogenase Gnd1

He, W., Wang, Y., Liu, W., Zhou, C.Z.

(2007) BMC Struct Biol 7: 38-38

• PubMed: 17570834 
• DOI: 10.1186/1472-6807-7-38
• Primary Citation of Related Structures:  
  2P4Q


• PubMed Abstract: 
  

As the third enzyme of the pentose phosphate pathway, 6-phosphogluconate dehydrogenase (6PGDH) is the main generator of cellular NADPH. Both thioredoxin reductase and glutathione reductase require NADPH as the electron donor to reduce oxidized thioredoxin or glutathione (GSSG). Since thioredoxin and GSH are important antioxidants, it is not surprising that 6PGDH plays a critical role in protecting cells from oxidative stress. Furthermore the activity of 6PGDH is associated with several human disorders including cancer and Alzheimer's disease. The 3D structural investigation would be very valuable in designing small molecules that target this enzyme for potential therapeutic applications.

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences at Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase, decarboxylating 1	A	497	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: GND1 EC: 1.1.1.44
UniProt
Find proteins for P38720 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38720  Go to UniProtKB:  P38720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	B [auth A], C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.220 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.261	α = 90
b = 147.261	β = 90
c = 114.428	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-12 
• Released Date: 2007-07-24 
Deposition Author(s): He, W., Wang, Y., Liu, W., Zhou, C.Z.

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance