Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 120381.71 
• Atom Count: 8401 
• Residue Count: 1045 
• Unique protein chains: 1

3DX0

Golgi alpha-Mannosidase II in complex with Mannostatin A at pH 5.75

• DOI: 10.2210/pdb3DX0/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Drosophila melanogaster


• Deposited: 2008-07-23 Released: 2009-07-07 
• Deposition Author(s): Kuntz, D.A., Rose, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.186 
• R-Value Work: 0.160 

Literature

The molecular basis of inhibition of Golgi alpha-mannosidase II by mannostatin A.

Kuntz, D.A., Zhong, W., Guo, J., Rose, D.R., Boons, G.J.

(2009) Chembiochem 10: 268-277

• PubMed: 19101978 
• DOI: 10.1002/cbic.200800538
• Primary Citation of Related Structures:  
  3DX4, 3DX3, 3DX2, 3DX1


• PubMed Abstract: 
  

Mannostatin A is a potent inhibitor of the mannose-trimming enzyme, Golgi alpha-mannosidase II (GMII), which acts late in the N-glycan processing pathway. Inhibition of this enzyme provides a route to blocking the transformation-associated changes in cancer cell surface oligosaccharide structures. Here, we report on the synthesis of new Mannostatin derivatives and analyze their binding in the active site of Drosophila GMII by X-ray crystallography. The results indicate that the interaction with the backbone carbonyl of Arg876 is crucial to the high potency of the inhibitor-an effect enhanced by the hydrophobic interaction between the thiomethyl group and an aromatic pocket vicinal to the cleavage site. The various structures indicate that differences in the hydration of protein-ligand complexes are also important determinants of plasticity as well as selectivity of inhibitor binding.

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Organizational Affiliation: 

Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Alpha-mannosidase 2	A	1045	Drosophila melanogaster	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MSN	A	(1R,2R,3R,4S,5R)-4-AMINO-5-(METHYLTHIO)CYCLOPENTANE-1,2,3-TRIOL C6 H13 N O3 S BLOFGONIVNXZME-YDMGZANHSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MSN	Ki: 36 nM (99) BINDINGDB
MSN	Ki: 36 nM BINDINGMOAD
MSN	Ki: 36 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.186 
• R-Value Work: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 68.853	α = 90.00
b = 109.860	β = 90.00
c = 139.136	γ = 90.00

Software Package:

Software Name	Purpose
SAINT	data scaling
SADABS	data scaling
REFMAC	refinement
CNS	phasing
PROTEUM PLUS	data collection
SAINT	data reduction
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-23 
• Released Date: 2009-07-07 
• Deposition Author(s): Kuntz, D.A., Rose, D.R.

Revision History 

• Version 1.0: 2009-07-07
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Non-polymer description, Version format compliance