SWISS-MODEL Repository - Model Details

Model Overview
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Sequence
UniProt Q9V9U4 Deoxyhypusine hydroxylase (Deoxyhypusine dioxygenase)
Drosophila melanogaster (Fruit fly).
Database: Swiss-Prot (Reviewed) manually annotated and 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: 24 to 125
Based on template: [ 3ltj ]  
Sequence Identity [%]: 35%
Model date: 2014-04-11
Revision date: 2014-04-08

Quaternary structure information: [details]
Template (3ltj): 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 2014-04-08. 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                                 RFRA LFTLKNIGGG AAIEAISKAF
3ltjA     12    hhhhtdpekv emyiknlqdd syyv--rraa ayalgkigde raveplikal
                                                                      
TARGET                                       hhh hhhhhhh       hhhhhh 
3ltjA                 hhhh hhhhhhh     hhh  hhhh hhhhhhh    hhhhhhhhhh


TARGET    25    DDDSALLKHE LAYCLGQMQD AQALDILTKV LKDTTQEPMV RHEAAEAMGA
3ltjA     60    kdedawvrra aadalgqigd eraveplika lkd--edgwv rqsaavalgq
                                                                      
TARGET              hhhhhh hhhhhhhh    hhhhhhhhh        hhh hhhhhhhhhh
3ltjA               hhhhhh hhhhhhhh    hhhhhhhhh h      hhh hhhhhhhhhh


TARGET    75    IGHP-DVLPI LEEYKQ-DPV VEVAETCAIA  --------- ----------
3ltjA     108   igderavepl ikalkdedwf vriaaafalg eigderavep likalkdedg
                                                                      
TARGET          h     hhhh hhhh     h hhhhhhhhhh                      
3ltjA           h      hhh hhh     hh hhhhhhhhhh hh      hh hhhhh    h


TARGET          ---------- ---------- ---------- ---------- -----     
3ltjA     158   wvrqsaadal geiggervra ameklaetgt gfarkvavny lethk     
                                                                      
TARGET                                                                
3ltjA           hhhhhhhhhh hh   hhhhh hhhhhhh     hhhhhhhhh hhh       



Quality


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


Quaternary Structure Annotation of the Template
3ltj is annotated as MONOMER
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: 3ltj.pdb1.gz

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 0.258 (>0.5 indicates similarity)


Template Selection
 - Start SMR-Pipeline for:d271eca168a25ec9c2c9c77892294cd6 on BC2-cluster at Fri Apr 11 02:39:13
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: 
 - 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:5): model based on new templates
 - Send 5 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -       ***************************
 - building model based on 3ltjA (24-125) was successful 
 -            ***********************************************
 - building model based on 3ltjA (40-217) was successful 
 -                                                                 ***********
 - building model based on 4cr2Z (240-282) was successful 
 -             ********************************************************************
 - building model based on 4cr2Z (44-301) was successful 
 -   *************************************************************************
 - building model based on 4cr2Z (6-282) 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 Apr 11 02:41:40
2014 




Template Description
Match Chain SeqId

4cr4: DEEP CLASSIFICATION OF A LARGE CRYO-EM DATASET DEFINES THECONFORMATIONAL LANDSCAPE OF THE 26S PROTEASOME
Solved by: X-RAY, Resolution: 8.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

24-295 4cr4Z 12%
[Model]
6-282 4cr4Z 11%
[Model]
4-248 4cr4Z 7%
[Model]
44-301 4cr4Z 13%
[Model]
197-215 4cr4Z 11%
[Model]
178-281 4cr4Z 10%
[Model]
162-288 4cr4Z 12%
[Model]
89-263 4cr4Z 13%
[Model]
209-290 4cr4Z 11%
[Model]
240-282 4cr4Z 20%
[Model]
3-216 4cr4Z 11%
[Model]

4cr3: DEEP CLASSIFICATION OF A LARGE CRYO-EM DATASET DEFINES THECONFORMATIONAL LANDSCAPE OF THE 26S PROTEASOME
Solved by: X-RAY, Resolution: 8.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

24-295 4cr3Z 12%
[Model]
6-282 4cr3Z 11%
[Model]
4-248 4cr3Z 7%
[Model]
44-301 4cr3Z 13%
[Model]
197-215 4cr3Z 11%
[Model]
178-281 4cr3Z 10%
[Model]
162-288 4cr3Z 12%
[Model]
89-263 4cr3Z 13%
[Model]
209-290 4cr3Z 11%
[Model]
240-282 4cr3Z 20%
[Model]
3-216 4cr3Z 11%
[Model]

4cr2: DEEP CLASSIFICATION OF A LARGE CRYO-EM DATASET DEFINES THECONFORMATIONAL LANDSCAPE OF THE 26S PROTEASOME
Solved by: X-RAY, Resolution: 8.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

24-295 4cr2Z 12%
[Model]
6-282 4cr2Z 11%
[Model]
4-248 4cr2Z 7%
[Model]
44-301 4cr2Z 13%
[Model]
197-215 4cr2Z 11%
[Model]
178-281 4cr2Z 10%
[Model]
162-288 4cr2Z 12%
[Model]
89-263 4cr2Z 13%
[Model]
209-290 4cr2Z 11%
[Model]
240-282 4cr2Z 20%
[Model]
3-216 4cr2Z 11%
[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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