SWISS-MODEL Repository - Model Details

Model Overview
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1
302

Sequence
UniProt Q9V9U4
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9V9U4: 7227.FBpp0085222

Domain
Link to: [ InterPro ]
HEAT_PBS
HEAT_PBS
HEAT_PBS
HEAT_PBS
HEAT_PBS

Model 3D Structure
Model information:
Modelled residue range: 1 to 284
Based on template: [ 4d4z ]  
Sequence Identity [%]: 59%
Model date: 2015-05-08
Revision date: 2015-05-05

Quaternary structure information: [details]
Template (4d4zB): Unknown
Model: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: FE: 2, GOL: 1, OH: 1.
Ligands in the model: FE: 2
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

TARGET    1            MVS QQQIEAIGGV LNNKERPLKE RFRALFTLKN IGGGAAIEAI
4d4zB     65531  gplgs--mvt eqevdaigqt lvdpkqplqa rfralftlrg lggpgaiawi
                                                                      
TARGET                  hh hhhhhhhhhh h      hhh hhhhhhhhhh    hhhhhhh
4d4zB             hhh  hhh hhhhhhhhhh h      hhh hhhhhhhhhh    hhhhhhh


TARGET    44    SKAFDDDSAL LKHELAYCLG QMQDAQALDI LTKVLKDTTQ EPMVRHEAAE
4d4zB     44    sqafdddsal lkhelayclg qmqdaraipm lvdvlqdtrq epmvrheage
                                                                      
TARGET          h       hh hhhhhhhhhh h       hh hhhhhh      hhhhhhhhh
4d4zB           h       hh hhhhhhhhhh h    hhhhh hhhhhh      hhhhhhhhh


TARGET    94    AMGAIGHPDV LPILEEYKQD PVVEVAETCA IALDRVRWLQ SGQKVDDSNP
4d4zB     94    algaigdpev leilkqyssd pvievaetcq lavrrlewlq qhggepaagp
                                                                      
TARGET          hhhh        hhhhhh      hhhhhhhh hhhhhhhhhh hh        
4d4zB           hhhh        hhhhhh      hhhhhhhh hhhhhhhhhh hh        


TARGET    144   YASVDPSPPT AGDKSVTELK AIYLDAQQSL FDRYRAMFSL RNLRTEESVL
4d4zB     144   ylsvdpapp- aeerdvgrlr ealldesrpl feryramfal rnaggeeaal
                                                                      
TARGET                          hhhhh hhhh     h hhhhhhhhhh hh   hhhhh
4d4zB                           hhhhh hhhh     h hhhhhhhhhh hh   hhhhh


TARGET    194   AIAEGLKDSS ALFRHEVAFV LGQLQEPCSI PFLQENLEDR LENEMVRHEC
4d4zB     193   alaeglhcgs alfrhevgyv lgqlqheaav pqlaaalarc tenpmvrhec
                                                                      
TARGET          hhhhh      hhhhhhhhhh hhhh   hhh hhhhhhhh      hhhhhhh
4d4zB           hhhhh      hhhhhhhhhh hhhh   hhh hhhhhhhh      hhhhhhh


TARGET    244   AEALGAIATE DCIQILNRYA EDDKRVVKES CVIALDMCEY E -       
4d4zB     243   aealgaiarp aclaalqaha ddpervvres cevaldmyeh etg       
                                                                      
TARGET          hhhhhhh    hhhhhhh        hhhhhh hhhhhhhhhh h         
4d4zB           hhhhhhh    hhhhhhh        hhhhhh hhhhhhhhhh hh        



Quality


Template's ligands section
Ligands in the template: FE: 2, GOL: 1, OH: 1.
Ligands in the template that will be assessed: FE301, FE302.
Model's ligands section
FE301
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.070
Given the properties calculated previously, the ligand B.FE301 will be included in the final model.
FE301: conservation:True, RMSD:True, included: True

FE302
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.060
Given the properties calculated previously, the ligand B.FE302 will be included in the final model.
FE302: conservation:True, RMSD:True, included: True

The new model with the included ligands was saved successfully.


Oligomer Annotation of the Template structure
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:d271eca168a25ec9c2c9c77892294cd6 on BC2-cluster at Fri May  8 15:26:31
2015 


 - 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: 
 - No template with A found
 - No template with A 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 4d4zB (1-284) 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:d271eca168a25ec9c2c9c77892294cd6 on BC2-cluster at Fri May  8 15:28:10
2015 




Template Description
Match Chain SeqId

4uae: IMPORTIN ALPHA 3 DELTA IBB IN COMPLEX WITH INFLUENZA PB2 NLOCALIZATION DOMAIN
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

6-281 4uaeA 10%
[Model]
6-281 4uaeA 10%
[Model]
39-287 4uaeA 10%
[Model]
4-217 4uaeA 9%
[Model]
70-282 4uaeA 11%
[Model]
5-129 4uaeA 10%
[Model]
4-248 4uaeA 7%
[Model]
103-281 4uaeA 8%
[Model]
6-17 4uaeA 17%
[Model]
156-282 4uaeA 11%
[Model]
275-288 4uaeA 0%
[Model]
6-127 4uaeA 13%
[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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