2IZ0

PEX inhibitor-home data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1111/j.1742-4658.2006.05585.x
  • Primary Citation of Related Structures:  
    2IYP, 2IZ1, 2IYO, 2IZ0

  • 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 liv ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATINGABC474Lactococcus lactisMutation(s): 0 
EC: 1.1.1.44
Find proteins for P96789 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore P96789 
Go to UniProtKB:  P96789
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

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A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
ATR
Query on ATR

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B, C
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
YPTPYQSAVGGMFN-KQYNXXCUSA-N
 Ligand Interaction
P33
Query on P33

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A, C
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
RES
Query on RES

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A
4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID
C4 H10 N O8 P
JJQQOJRGUHNREK-PWNYCUMCSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.126 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.957α = 90
b = 104.459β = 98.52
c = 241.478γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance