SWISS-MODEL Repository - Model Details

Model Overview
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1
756

Sequence
UniProt Q08AE8
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]

Model 3D Structure
Model information:
Modelled residue range: 34 to 236
Based on template: [ 2yle ]  
Sequence Identity [%]: 83%
Model date: 2013-02-12
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2yle): 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       GGSRDALS LEEILRLYNQ PINEEQAWAV CYQCCGSLRA AARRRQPRHR
2yleA     34      gssrdals leeilrlynq pineeqawav cyqccgslra aarrrqprhr
                                                                      
TARGET                ssss shhhhhhh      hhhhhhh hhhhhhhhhh hhh       
2yleA                 ssss shhhhhhh      hhhhhhh hhhhhhhhhh hhh       


TARGET    49    VRSAAQIRVW RDGAVTLAPA ADDAGEPPPV AGKLGYSQCM ETEVIESLGI
2yleA     82    vrsaaqirvw rdgavtlapa ---------- --klgysqcm etevieslgi
                                                                      
TARGET               sssss s  sssss                          hhhhhhhhh
2yleA                sssss s  sssss                         hhhhhhhhhh


TARGET    99    IIYKALDYGL KENEERELSP PLEQLIDHMA NTVEADGSND EGYEAAEEGL
2yleA     132   iiykaldygl keneerelsp pleqlidhma ntve------ ----------
                                                                      
TARGET          hhhhhhh             h hhhhhhhhhh            sssss  sss
2yleA           hhhhhhh             h hhhhhhhhhh                      


TARGET    149   GDEDEKRKIS AIRSYRDVMK LCAAHLPTES DAPNHYQAVC RALFAETMEL
2yleA     186   ----ekrkis airsyrdvmk lcaahlptes dapnhyqavc ralfaetmel
                                                                      
TARGET          ss             hhhhhh hhhh     h hhhhhhhhhh hhhhhhhhhh
2yleA                          hhhhhh hhhh     h hhhhhhhhhh hhhhhhhhhh


TARGET    199   HTFLT                                                 
2yleA     232   htflt-                                                
                                                                      
TARGET          hh                                                    
2yleA           hh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 2yle 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: 2yle.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 2yle_1

Template Selection 
 - Start SMR-Pipeline for:1d670f707615118e22c0645ed379710b on BC2-cluster at Tue Feb 12 10:08:22
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

FATAL - No A3m found

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B 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 2yleA (34-236) 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:1d670f707615118e22c0645ed379710b on BC2-cluster at Tue Feb 12 10:10:02
2013


Template Description
Match Chain SeqId

2yle: CRYSTAL STRUCTURE OF THE HUMAN SPIR-1 KIND FSI DOMAIN IN COMPLEX WITH THE FSI PEPTIDE
Solved by: X-RAY, Resolution: 1.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

34-236 2yleA 84%
[Model]

2ylf: CRYSTAL STRUCTURE OF THE HUMAN SPIR-1 KIND DOMAIN
Solved by: X-RAY, Resolution: 2.05A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

37-235 2ylfA 81%
[Model]

3r7g: CRYSTAL STRUCTURE OF SPIRE KIND DOMAIN IN COMPLEX WITH THEFMN2
Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

37-231 3r7gA 79%
[Model]

3rbw: CRYSTAL STRUCTURE OF SPIRE KIND DOMAIN
Solved by: X-RAY, Resolution: 3.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

38-232 3rbwA 79%
[Model]
38-232 3rbwB 79%
[Model]
37-232 3rbwC 77%
[Model]
37-231 3rbwD 76%
[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.