SWISS-MODEL Repository - Model Details

Model Overview
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Sequence
UniProt O09159
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Glyco_hydro_38
Glyco_hydro_38C
Alpha-mann_mid

Model 3D Structure
Model information:
Modelled residue range: 349 to 421
Based on template: [ 1o7d ]  
Sequence Identity [%]: 90%
Model date: 2013-02-17
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1o7d): HETERO PENTAMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: NAG: 1.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-01-30. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment 

TARGET    1         VHVLYS TPTCYLWELN KANLTWTVKE DDFFPYADGP HMFWTGYFSS
1o7dB     347   ir--vnvlys tpacylweln kanlswsvkk ddffpyadgp ymfwtgyfss
                                                                      
TARGET                      hhhhhhhhh h                               
1o7dB                       hhhhhhhhh h                          hh   


TARGET    47    RPALKRYERL SYNFLQVCNQ LEALVGP                         
1o7dB     395   rpalkryerl synflqvcnq lealagp-                        
                                                                      
TARGET           hhhhhhhhh hhhhhhhhhh hhhh                            
1o7dB            hhhhhhhhh hhhhhhhhhh hhhh

Quality 


Template's ligands section 
Ligands in the template: NAG: 1. 
Ligands in the template that will be assessed: NAG2. 
Model's ligands section 
NAG2 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand C.NAG2 will not be included in the model. 
NAG2: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 1o7d is annotated as HETERO PENTAMER 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 1o7d.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 1o7d_1

Template Selection 
 - Start SMR-Pipeline for:959af0167b33993f55270efe4c68043f on BC2-cluster at Sun Feb 17 18:43:19
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  5 go for
modeling ...

FATAL - No A3m found

 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with E found
 - No template with A found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with A found
 - No template with C found
 - No template with D found
 - No template with E found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:5): model based on new templates
 - Send 5 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                             ******
 - building model based on 1o7dB (349-421) was successful 
 -     ***********************
 - building model based on 1o7dA (51-341) was successful 
 -                                                 *********************
 - building model based on 1o7dD (606-875) was successful 
 -                                   ************
 - building model based on 1o7dC (431-583) was successful 
 -                                                                       **********
 - building model based on 1o7dE (886-1007) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:959af0167b33993f55270efe4c68043f on BC2-cluster at Sun Feb 17 18:44:56
2013


Template Description
Match Chain SeqId

1o7d: THE STRUCTURE OF THE BOVINE LYSOSOMAL A-MANNOSIDASE SUGGESTS A NOVEL MECHANISM FOR LOW PH ACTIVATION
Solved by: X-RAY, Resolution: 2.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

51-341 1o7dA 79%
[Model]
606-875 1o7dD 74%
[Model]
431-583 1o7dC 69%
[Model]
886-1007 1o7dE 66%
[Model]
349-421 1o7dB 90%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.