Golgi alpha-mannosidase II complex with 5-thio-D-mannopyranosylamine

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 

This is version 2.2 of the entry. See complete history


5-Thio-d-glycopyranosylamines and their amidinium salts as potential transition-state mimics of glycosyl hydrolases: synthesis, enzyme inhibitory activities, X-ray crystallography, and molecular modeling

Kavelekar, L.M.Kuntz, D.A.Xin, W.Johnston, B.D.Svensson, B.Rose, D.R.Pinto, B.M.

(2005) Tetrahedron Asymmetry 16: 1035-1046

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative golgi alpha-mannosidase II1,045Drosophila melanogasterMutation(s): 0 
Gene Names: ALPHA-MAN-II OR GMII OR CG18474/CG18802/CG8139
Find proteins for Q24451 (Drosophila melanogaster)
Explore Q24451 
Go to UniProtKB:  Q24451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24451
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LKA Binding MOAD:  1R33 IC50: 7.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.838α = 90
b = 109.911β = 90
c = 138.891γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-05-13
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.2: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary