1TQU

Golgi alpha-Mannosidase II In Complex With The Salacinol Analog Ghavamiol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystallographic analysis of the interactions of Drosophila melanogaster Golgi alpha-mannosidase II with the naturally occurring glycomimetic salacinol and its analogues

Kuntz, D.A.Ghavami, A.Johnston, B.D.Pinto, B.M.Rose, D.R.

(2005) Tetrahedron Asymmetry 16: 25-32


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-mannosidase IIA1045Drosophila melanogasterMutation(s): 0 
Gene Names: ALPHA-MAN-IIGmIICG18474/CG18802/CG8139alpha-Man-IIaCG18802
EC: 3.2.1.114
UniProt
Find proteins for Q24451 (Drosophila melanogaster)
Explore Q24451 
Go to UniProtKB:  Q24451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24451
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GHA
Query on GHA

Download Ideal Coordinates CCD File 
D [auth A]1'-((1,4-DIDEOXY-1,4-IMINO-D-ARABINITOL)-4-N-AMMONIUM)-1'-DEOXY-L-ERYTHRITOL-3'-SULFATE INNER SALT
C9 H18 N O9 S
YWOSRVQDYDWMAB-JBXPSPKUSA-K
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MRD
Query on MRD

Download Ideal Coordinates CCD File 
E [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GHA Binding MOAD:  1TQU IC50: 7.50e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.298α = 90
b = 108.957β = 90
c = 137.723γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary