2OW6

Golgi alpha-mannosidase II complex with (1r,5s,6s,7r,8s)-1-thioniabicyclo[4.3.0]nonan-5,7,8-triol chloride

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Binding of sulfonium-ion analogues of di-epi-swainsonine and 8-epi-lentiginosine to Drosophila Golgi alpha-mannosidase II: The role of water in inhibitor binding.

Kumar, N.S., Kuntz, D.A., Wen, X., Pinto, B.M., Rose, D.R.

(2008) Proteins 71: 1484-1496

  • DOI: 10.1002/prot.21850
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Retaining glycosidases operate by a two-step catalytic mechanism in which the transition states are characterized by buildup of a partial positive charge at the anomeric center. Sulfonium-ion analogues of the naturally occurring glycosidase inhibitor ...

    Retaining glycosidases operate by a two-step catalytic mechanism in which the transition states are characterized by buildup of a partial positive charge at the anomeric center. Sulfonium-ion analogues of the naturally occurring glycosidase inhibitors, swainsonine and 8-epi-lentiginosine, in which the bridgehead nitrogen atom is replaced by a sulfonium-ion, were synthesized in order to test the hypothesis that a sulfonium salt carrying a permanent positive charge would be an effective glycosidase inhibitor. Initial prediction based on computational docking indicated three plausible binding modes to Drosophila Golgi alpha-mannosidase II (dGMII), the most likely being close to that of swainsonine. Observation of the binding of di-epi-thioswainsonine and 8-epi-thiolentiginosine to dGMII from crystallographic data, however, revealed an orientation different from swainsonine in the active site. Screening these two compounds against dGMII shows that they are inhibitors with IC(50) values of 2.0 and 0.014 mM, respectively. This dramatic difference in affinity between the two compounds, which differ by only one hydroxyl group, is rationalized in terms of bound water molecules and the water molecule substructure in the active site, as identified by comparison of high resolution X-ray crystal structures of several dGMII-inhibitor complexes.

    Organizational Affiliation: 

    Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-mannosidase 2
A
1045Drosophila melanogasterMutation(s): 0 
Gene Names: alpha-Man-IIa (GmII)
EC: 3.2.1.114
Find proteins for Q24451 (Drosophila melanogaster)
Go to UniProtKB:  Q24451
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD
Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
NK1
Query on NK1
Download SDF File 
Download CCD File 
A
(1R,5S,6S,7R,8S)-1-THIONIABICYCLO[4.3.0]NONAN-5,7,8-TRIOL
C8 H15 O3 S
YXHBFMXISHCSIQ-OZFRBSTCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NK1IC50: 2000000 nM BINDINGMOAD
NK1IC50: 2000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.118 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.007α = 90.00
b = 109.620β = 90.00
c = 138.915γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
ADSCdata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2007-02-15 
  • Released Date: 2008-01-08 
  • Deposition Author(s): Kuntz, D.A.

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description