SWISS-MODEL Repository - Model Details

Model Overview
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1
250

Sequence
UniProt Q9LSS3
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
tRNA_int_endo
tRNA_int_endo_N

Model 3D Structure
Model information:
Modelled residue range: 116 to 209
Based on template: [ 3p1z ]  
Sequence Identity [%]: 36%
Model date: 2013-02-20
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3p1z): HETERO TETRAMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: none.
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 

                                                       
3p1zL     3     drcapikasg vligdsvlvt dveqarslys cgyygqpldv ekprgadfeg
                                                                      
                                                       
3p1zL                  sss ss    sss    hhhhhhhh h    sss             


TARGET    1                                                 PNFPMFFKAY
3p1zL     53    plrlsliesl ylaekgvlev akpdgssvgv edlrtavrgn prfsmlyniy
                                                                      
TARGET                                                       hhhhhhhhh
3p1zL           ssss hhhhh hhhhh   ss ss   sss     hhhhh    hhhhhhhhhh


TARGET    11    SHLRSKNWVL RSGLQYGVDF VAYRHHPSLV HSEYSVLVQS GDSDRLRVWS
3p1zL     103   rdlrergfvv rsglkfgsdf avyrlgpgid hapfivhays pednidpv--
                                                                      
TARGET          hhhhhh  ss sss     ss sss           ssssss            
3p1zL           hhhhhh  ss sss     ss sss           ssssss         h  


TARGET    61    DIHCAVRLSG SVAKTLLTLY VNGNFKGEDV NLLV -----           
3p1zL     151   eivragrlsh svrkk----f vfavtrggdv sylmidwfrp           
                                                                      
TARGET          hhhhhhh             s sssss      ssss                 
3p1zL           hhhhhhh             s sssss      sssss

Quality 


Template's ligands section 
Template without ligands. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3p1z is annotated as HETERO TETRAMER 
 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: 3p1z.pdb3.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3p1z_3

Template Selection 
 - Start SMR-Pipeline for:998d81823e34d56afcc1ca5d417bdffe on BC2-cluster at Wed Feb 20 01:10:25
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with A found
 - No template with I found
 - No template with K found
 - No template with E found
 - No template with G found
 - No template with A found
 - No template with C found
 - No template with A found
 - No template with C found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                      ******************************
 - building model based on 3p1zL (116-209) was successful 
 -                      ******************************************
 - building model based on 2cv8B (67-197) 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:998d81823e34d56afcc1ca5d417bdffe on BC2-cluster at Wed Feb 20 01:12:23
2013

no data available!
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.
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