SWISS-MODEL Repository - Model Details

Model Overview
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1
202

Sequence
UniProt P09225
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P09225: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
TNF

Model 3D Structure
Model information:
Modelled residue range: 59 to 202
Based on template: [ 1tnr ]  
Sequence Identity [%]: 79%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1tnr): HETERO DIMER
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 

TARGET    1       KPAAHLVG YPSKQNSLLW RASTDRAFLR HGFSLSNNSL LIPTSGLYFV
1tnrA     28      kpaahlig dpskqnsllw rantdraflq dgfslsnnsl lvptsgiyfv
                                                                      
TARGET             sssssss s       ss s      sss    sss  ss ss   sssss
1tnrA              sssssss s       ss s      sss    sss  ss ss   sssss


TARGET    49    YSQVVFSGES CSPRAIPTPI YLAHEVQLFS SQYPFHVPLL SAQKSVYPGL
1tnrA     76    ysqvvfsgka yspkatsspl ylahevqlfs sqypfhvpll ssqkmvypgl
                                                                      
TARGET          ssssssss      hhh   s sssssssss        ssss ssssss    
1tnrA           ssssssss      hhh   s sssssssss        ssss ssssss    


TARGET    99    QGPWVRSMYQ GAVFLLSKGD QLSTHTDGIS HLHFSPSSVF FGAFAL    
1tnrA     126   qepwlhsmyh gaafqltqgd qlsthtdgip hlvlspstvf fgafal-   
                                                                      
TARGET             sssssss ssssss   s sssssss    sss     ss ssssss    
1tnrA              sssssss ssssss   s sssssss    sss     ss ssssss

Quality 


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

 
Quaternary Structure Annotation of the Template 
 1tnr is annotated as HETERO 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: 1tnr.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 1tnr_1

Template Selection 
 - Start SMR-Pipeline for:491ec3cd91ed74fdf5b6114b92891d01 on BC2-cluster at Fri Feb 22 12:02:45
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with R found
 - No template with S found
 - No template with T found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with R found
 - No template with R found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with D found
 - No template with D found
 - No template with D found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                        *********************************************************
 - building model based on 1tnrA (59-202) 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:491ec3cd91ed74fdf5b6114b92891d01 on BC2-cluster at Fri Feb 22 12:04:53
2013


Template Description
Match Chain SeqId

1tnr: CRYSTAL STRUCTURE OF THE SOLUBLE HUMAN 55 KD TNF RECEPTOR-HUMAN TNF-BETA COMPLEX: IMPLICATIONS FOR TNF RECEPTOR ACTIVATION
Solved by: X-RAY, Resolution: 2.85A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

59-202 1tnrA 80%
[Model]

4f3j: CRYSTAL STRUCTURE OF TRIMERIC GC1Q DOMAIN OF HUMAN C1QTNF5WITH LATE-ONSET RETINAL MACULAR DEGENERATION
Solved by: X-RAY, Resolution: 1.34A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

72-202 4f3jA 10%
[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.