Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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: 55001.40 
• Atom Count: 3708 
• Residue Count: 497 
• Unique protein chains: 1

2P4Q

Crystal Structure Analysis of Gnd1 in Saccharomyces cerevisiae

• DOI: 10.2210/pdb2P4Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli


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

---

Experimental Data Snapshot

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


• 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.

---

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

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FLC	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 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 147.261	α = 90.00
b = 147.261	β = 90.00
c = 114.428	γ = 120.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance