SWISS-MODEL Repository - Model Details

Model Overview
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1
341

Sequence
UniProt P41374
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P41374: 7227.FBpp0074075

Domain
Link to: [ InterPro ]
S1
EIF_2_alpha

Model 3D Structure
Model information:
Modelled residue range: 3 to 301
Based on template: [ 1q8k ]  
Sequence Identity [%]: 61%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1q8k): MONOMER
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       LTSRFYNE RYPEIEDVVM VNVLSIAEMG AYVHLLEYNN IEGMILLSEL
1q8kA     3       mscrfyqh kfpevedvvm vnvrsiqemg ayvslleynn iegmihlsel
                                                                      
TARGET                           ssss sssssss  s ssssss   s ssssss    
1q8kA                            ssss sssssss  s sssss      ssssss    


TARGET    49    SRRRIRSINK LIRVGKTEPV VVIRVDKEKG YIDLSKRRVS PEDVEKCTER
1q8kA     51    srrrirsink lirigrnecv kvirvdkekg yidlskrrvs peeaikcedk
                                                                      
TARGET                            sss ssssss     sssss      hhhhhhhhhh
1q8kA                             sss ssssss     sssss      hhhhhhhhhh


TARGET    99    FAKAKAINSL LRHVADILGF EGNEKLEDLY QKTAWHFEKK YNNKTVA-YD
1q8kA     101   ftksktvysi lrhvaevley tkdeqleslf qrtawvfddk ykrpgygayd
                                                                      
TARGET          hhhhhhhhhh hhhhhhhh      hhhhhhh    hhhhhhh         hh
1q8kA           hhhhhhhhhh hhhhhhhh      hhhhhh    hhhhhhhh      hhhhh


TARGET    148   IFKQSVTDPT VFDECNLEPE TKEVLLSNIK RKLVSPTVKI RADIECSCYG
1q8kA     151   afkhavsdps ildsldlned erevlinnin rrltpqavki radievacyg
                                                                      
TARGET          hhhhh              hh hhhhhhhhhh hh     sss sssssss   
1q8kA           hhhhh              hh hhhhhhhhhh h      sss sssssss   


TARGET    198   YEGIDAVKAS LTKGLELSTE ELPIRINLIA PPLYVMTTST TKKTDGLKAL
1q8kA     201   yegidavkea lraglncste nmpikinlia ppryvmtttt lerteglsvl
                                                                      
TARGET           hhhhhhhhh hhhhhh       sssss       sssssss    hhhhhhh
1q8kA            hhhhhhhhh hhhhhh       sssss       sssssss    hhhhhhh


TARGET    248   EVAIEHIRAK TSEYDGEFKV IMAPKLVTAI DEADLARRLE RAEAENAQVA
1q8kA     251   sqamavikek ieekrgvfnv qmepkvvtdt detelarqme rlerenaevd
                                                                      
TARGET          hhhhhhhhhh       ssss s   sss  h hhhhhh               
1q8kA           hhhhhhhhhh       ssss s   sss  h hhh   h              


TARGET    298   GD                                                    
1q8kA     301   gd-                                                   
                                                                      
TARGET                                                                
1q8kA

Quality 


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

 
Quaternary Structure Annotation of the Template 
 1q8k is annotated as MONOMER 
 The template structure (1q8k) was solved by NMR and does not contain any quaternary structure annotation 
 The template is annotated by the number of chains found in the PDB file 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.13 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:e3f0b632583d5204c5d718cb0d2136ca on BC2-cluster at Fri Feb 22 11:02:59
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

FATAL - No A3m 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 1q8kA (3-301) 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:e3f0b632583d5204c5d718cb0d2136ca on BC2-cluster at Fri Feb 22 11:04:12
2013


Template Description
Match Chain SeqId

1q8k: SOLUTION STRUCTURE OF ALPHA SUBUNIT OF HUMAN EIF2
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-301 1q8kA 61%
[Model]

1q46: CRYSTAL STRUCTURE OF THE EIF2 ALPHA SUBUNIT FROM SACCHAROMYCES CEREVISIA
Solved by: X-RAY, Resolution: 2.86A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

6-174 1q46A 60%
[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.