2IZ1

6PDH complexed with PEX inhibitor synchrotron data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of a Bacterial 6- Phosphogluconate Dehydrogenase Reveal Aspects of Specificity, Mechanism and Mode of Inhibition by Analogues of High-Energy Reaction Intermediates.

Sundaramoorthy, R.Iulek, J.Barrett, M.P.Bidet, O.Ruda, G.F.Gilbert, I.H.Hunter, W.N.

(2007) FEBS J 274: 275

  • DOI: https://doi.org/10.1111/j.1742-4658.2006.05585.x
  • Primary Citation of Related Structures:  
    2IYO, 2IYP, 2IZ0, 2IZ1

  • PubMed Abstract: 

    Crystal structures of recombinant Lactococcus lactis 6-phosphogluconate dehydrogenase (LlPDH) in complex with substrate, cofactor, product and inhibitors have been determined. LlPDH shares significant sequence identity with the enzymes from sheep liver and the protozoan parasite Trypanosoma brucei for which structures have been reported. Comparisons indicate that the key residues in the active site are highly conserved, as are the interactions with the cofactor and the product ribulose 5-phosphate. However, there are differences in the conformation of the substrate 6-phosphogluconate which may reflect distinct states relevant to catalysis. Analysis of the complex formed with the potent inhibitor 4-phospho-d-erythronohydroxamic acid, suggests that this molecule does indeed mimic the high-energy intermediate state that it was designed to. The analysis also identified, as a contaminant by-product of the inhibitor synthesis, 4-phospho-d-erythronamide, which binds in similar fashion. LlPDH can now serve as a model system for structure-based inhibitor design targeting the enzyme from Trypanosoma species.


  • Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
A, B, C
474Lactococcus lactisMutation(s): 0 
EC: 1.1.1.44
UniProt
Find proteins for P96789 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore P96789 
Go to UniProtKB:  P96789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96789
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATR
Query on ATR

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
K [auth C]
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
YPTPYQSAVGGMFN-KQYNXXCUSA-N
P33
Query on P33

Download Ideal Coordinates CCD File 
F [auth A],
N [auth C]
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
RES
Query on RES

Download Ideal Coordinates CCD File 
E [auth A]4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID
C4 H10 N O8 P
JJQQOJRGUHNREK-PWNYCUMCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
L [auth C],
M [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.069α = 90
b = 104.879β = 98.31
c = 240.542γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Other, Structure summary