SWISS-MODEL Repository - Model Details

Model Overview
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Sequence
UniProt P08F94
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P08F94: 9606.ENSP0000036

Domain
Link to: [ InterPro ]
TIG
TIG
TIG
TIG
TIG
TIG
TIG
G8
G8
Beta_helix
Beta_helix

Model 3D Structure
Model information:
Modelled residue range: 1389 to 1414
Based on template: [ 4qt8 ]  
Sequence Identity [%]: 26%
Model date: 2014-10-08
Revision date: 2014-10-06

Quaternary structure information: [details]
Template (4qt8A): Unknown
Model: 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 ]

Alignment

                                                       
4qt8A     28    qcprtpyaas rdfdvkyvvp sfsagglvqa mvtyegdrne savfvairnr
                                                                      
                                                       
4qt8A                    s ss          sss     s ssssss   s sssssss ss


                                                       
4qt8A     78    lhvlgpdlks vqslatgpag dpgcqtcaac gpgphgppgd tdtkvlvldp
                                                                      
                                                       
4qt8A           sssss   ss ssssss         hhhhh              ssssssss 


                                                       
4qt8A     128   alpalvscgs slqgrcflhd lepqgtavhl aapaclfsah hnrpddcpdc
                                                                      
                                                       
4qt8A              sssssss       ssss ssss  ssss s                    


                                                       
4qt8A     178   vasplgtrvt vveqgqasyf yvassldaav agsfsprsvs irrlkadasg
                                                                      
                                                       
4qt8A                  sss ssss  ssss ssss              sss sssss    s


                                                       
4qt8A     228   fapgfvalsv lpkhlvsysi eyvhsfhtga fvyfltvqpa svtddpsalh
                                                                      
                                                       
4qt8A           ss                    ssssssss s ssssssssss        sss


                                                       
4qt8A     278   trlarlsate pelgdyrelv ldcrfapklv prgspeggqp ypvlqvahsa
                                                                      
                                                       
4qt8A           ssssssss      sssssss sssss              ss s ssssssss


                                                       
4qt8A     328   pvgaqlatel siaegqevlf gvfvtgkdgg gpnsvvcafp idlldtlide
                                                                      
                                                       
4qt8A              hhhh          ssss ssss           ssssss shhhhhhhhh


                                                       
4qt8A     381   gverccespv hpglrrgldf fqspsfcpnp pglealspnt scrhfpllvs
                                                                      
                                                       
4qt8A           hhhhh                                           sssss 


                                                       
4qt8A     431   ssfsrvdlfn gllgpvqvta lyvtrldnvt vahmgtmdgr ilqvelvrsl
                                                                      
                                                       
4qt8A             sssss          ssss ssssss  ss sssssss ss ssssss    


                                                       
4qt8A     481   nyllyvsnfs lgdsgqpvqr dvsrlgdhll fasgdqvfqv piqgpgcrhf
                                                                      
                                                       
4qt8A              sssssss s            sss ssss sss ssssss ss      ss


TARGET    1                                              PR IMAIFPSQGS
4qt8A     531   ltcgrclraw hfmgcgwcgn mcgqqkecpg swqqdhcppk ltefhphsgp
                                                                      
TARGET                                                    s sssss     
4qt8A           s   h           sss   sss                 s sssss     


TARGET    13    ACGGTILTVR GLLL ----- ---------- ---------- ----------
4qt8A     581   l--strltlc gsnfylhpeg thqvtvgqsp crplpfveef eceleplgpt
                                                                      
TARGET                 sss ss                                         
4qt8A               ssssss ss            sss      sss   sss ssss      


TARGET          ---------- ---------- ----------                      
4qt8A     654   nvsltvtnmp pgkhfrvdgt svlrgfsfme                      
                                                                      
TARGET                                                                
4qt8A             sss                                                 



Quality


Template's ligands section
Ligands in the template: NAG: 1.
Ligands in the template that will be assessed: NAG701.
Model's ligands section
NAG701
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand A.NAG701 will not be included in the model.
NAG701: conservation:False, RMSD:False, included: False

No ligands were included in the model.


Sorry, we haven't found any oligomeric annotation for this template. 
Either the complex was too large (>60 chains) or the structures was excluded for other reasons.
Please contact help@swissmodel.org for more information!


Template Selection
 - Start SMR-Pipeline for:5184e3c25d6453985fe161a12d4fc113 on BC2-cluster at Wed Oct  8 12:10:14
2014 


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

 - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - Warning: Oligomer Prediction was not successfull!

 - Warning: clustersMergedFile not found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:8): model based on new templates
 - Send 8 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                            *
 - building model based on 4qt8A (1389-1414) was successful 
 -                         *
 - building model based on 4qt8A (1198-1253) was successful 
 -                           *
 - building model based on 4qt8B (1301-1338) was successful 
 -                                *
 - building model based on 4qt8A (1573-1628) was successful 
 -                     *
 - building model based on 4qt8B (1017-1077) was successful 
 -                                     *
 - building model based on 4qt8A (1844-1900) was successful 
 -                   **
 - building model based on 4qt8A (920-1000) was successful 
 -                       *
 - building model based on 4qt8A (1108-1178) 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:5184e3c25d6453985fe161a12d4fc113 on BC2-cluster at Wed Oct  8 12:12:39
2014 




Template Description
Match Chain SeqId

4qt8: CRYSTAL STRUCTURE OF RON SEMA-PSI-IPT1 EXTRACELLULAR DOMAICOMPLEX WITH MSP BETA-CHAIN
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

920-1000 4qt8A 16%
[Model]
920-1000 4qt8B 16%
[Model]
1016-1078 4qt8A 19%
[Model]
1108-1178 4qt8A 13%
[Model]
1573-1628 4qt8A 21%
[Model]
1389-1414 4qt8A 27%
[Model]
1844-1908 4qt8B 16%
[Model]
1017-1077 4qt8B 20%
[Model]
1108-1166 4qt8B 12%
[Model]
1844-1900 4qt8A 17%
[Model]
1198-1253 4qt8A 26%
[Model]
1573-1629 4qt8B 20%
[Model]
1300-1340 4qt8A 20%
[Model]
1201-1222 4qt8B 32%
[Model]
1301-1338 4qt8B 21%
[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.




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