SWISS-MODEL Repository - Model Details

Model Overview
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1
536

Sequence
UniProt Q6DFW4
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q6DFW4: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
Nop
NOSIC
NOP5NT

Model 3D Structure
Model information:
Modelled residue range: 157 to 320
Based on template: [ 3icx ]  
Sequence Identity [%]: 40%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3icx): DIMER
Model: DIMER

Ligand information: [details]
Ligands in the template: SO4: 4.
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       KVDTMIVQ AISLLDDLDK ELNNYIMRCR EWYGWHFPEL GKIISDNLTY
3icx_2#1  135     krdllaiq avramddidk tinlfserlr ewysihfpel dkliedheey
                                                                      
TARGET              hhhhhh hhhhhhhhhh hhhhhhhhhh hhhhh   hh hhh   hhhh
3icx_2#1            hhhhhh hhhhhhhhhh hhhhhhhhhh hhhhh   hh       hhhh


TARGET    49    CKCLQKVGDR KNYASASLSE F-LSEEVEAE VKAAAEISMG TEVSEEDICN
3icx_2#1  183   ativsrfgdr gfltidslke lgfneqrinr ildaakksig adiseddlsa
                                                                      
TARGET          hhhhhhh        hhhh        hhhhh hhhhhh         hhhhhh
3icx_2#1        hhhhhh         hhhhh      hhhhhh hhhhhh         hhhhhh


TARGET    98    ILHLCTQVIE ISEYRTQLYE YLQNRMMAIA PNVTVMVGEL VGARLIAHAG
3icx_2#1  233   mrmiantild lynirrnlnn ylegvmkeva pnvtalvgpa lgarllsiag
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh hhhhhhhh    hhhhh   h hhhhhhhh  
3icx_2#1        hhhhhhhhhh hhhhhhhhhh hhhhhhhh    hhhhh   h hhhhhhhh  


TARGET    148   SLLNLAKHAA STVQILG -- ---------- ---------- ----------
3icx_2#1  283   sldelakmpa stiqvlg-ii fqypaihtsp rwqrgkiara laaklaiaar
                                                                      
TARGET           hhhhh   h hhhhh                                      
3icx_2#1         hhhhh   h hhhh         hhhhh     hhhhhhhhh hhhhhhhhhh


TARGET    165   ---------- ---------- ---------  KVDTMIVQAI SLLDDLDKEL
3icx_2#1  351   vdafsgrfig dqlneqlkkr ideikekf-- krdllaiqav ramddidkti
                                              *                       
TARGET                                             hhhhhhhh hhhhhhhhhh
3icx_2#1        hhhh     h hhhhhhhhhh hhhhh        hhhhhhhh hhhhhhhhhh


TARGET    185   NNYIMRCREW YGWHFPELGK IISDNLTYCK CLQKVGDRKN YASASLSEF-
3icx_2#1  155   nlfserlrew ysihfpeldk liedheeyat ivsrfgdrgf ltidslkelg
                                                                      
TARGET          hhhhhhhhhh hhh   hhhh h   hhhhhh hhhhh        hhhh    
3icx_2#1        hhhhhhhhhh hhh   hh       hhhhhh hhhh         hhhhh   


TARGET    234   LSEEVEAEVK AAAEISMGTE VSEEDICNIL HLCTQVIEIS EYRTQLYEYL
3icx_2#1  205   fneqrinril daakksigad iseddlsamr miantildly nirrnlnnyl
                                                                      
TARGET            hhhhhhhh hhhh         hhhhhhhh hhhhhhhhhh hhhhhhhhhh
3icx_2#1          hhhhhhhh hhhh         hhhhhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    284   QNRMMAIAPN VTVMVGELVG ARLIAHAGSL LNLAKHAAST VQILG ----
3icx_2#1  255   egvmkevapn vtalvgpalg arllsiagsl delakmpast iqvlgiifqy
                                                                      
TARGET          hhhhhh   h hhhh   hhh hhhhhh   h hhhh   hhh hhh       
3icx_2#1        hhhhhh   h hhhh   hhh hhhhhh   h hhhh   hhh hh       h


TARGET          ---------- ---------- ---------- ---------- ----------
3icx_2#1  324   paihtsprwq rgkiaralaa klaiaarvda fsgrfigdql neqlkkride
                                                                      
TARGET                                                                
3icx_2#1        hhhh    hh hhhhhhhhhh hhhhhhhhhh h     hhhh hhhhhhhhhh


TARGET          -----                                                 
3icx_2#1  374   ikekf                                                 
                                                                      
TARGET                                                                
3icx_2#1        hh

Quality 


Template's ligands section 
Ligands in the template: SO4: 4. 
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3icx is annotated as DIMER 
 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: 3icx.pdb2.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=DIMER) 
 The corresponding reliability score is 0.65 (>0.5 indicates similarity) 
 Model was succesfully built as DIMER.

Template Selection 
 - Start SMR-Pipeline for:adfdb5ef2027d79743a90655bd1e9b03 on BC2-cluster at Sat Feb 23 02:18:02
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 D found
 - No template with A found
 - No template with C found
 - No template with J found
 - No template with F found
 - No template with G found
 - No template with B found
 - No template with C found
 - No template with F found
 - No template with G found
 - No template with B found
 - No template with B found
 - No template with D found
 - No template with D found
 - No template with A found
 - No template with D found
 - No template with G found
 - No template with J found
 - No template with L found
 - No template with M found
 - No template with L found
 - No template with M found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with B found
 - No template with A found
 - No template with D found
 - No template with C found
 - No template with C found
 - No template with E found
 - No template with H found
 - No template with I found
 - No template with J 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 3icxC (157-320) was successful 
 -                      ***************************************
 - building model based on 3plaK (142-401) 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:adfdb5ef2027d79743a90655bd1e9b03 on BC2-cluster at Sat Feb 23 02:20:20
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.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.