SWISS-MODEL Repository - Model Details

Model Overview
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1
760

Sequence
UniProt Q960X8
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q960X8: 7227.FBpp0088692

Domain
Link to: [ InterPro ]
VHS
FYVE
Hrs_helical

Model 3D Structure
Model information:
Modelled residue range: 1 to 219
Based on template: [ 1dvp ]  
Sequence Identity [%]: 98%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1dvp): DIMER
Model: DIMER

Ligand information: [details]
Ligands in the template: CIT: 2, MET: 2, ZN: 4.
Ligands in the model: ZN: 4
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       MFRSSFDK NLENATSHLR LEPDWPSILL ICDEINQKDV TPKNAFAAIK
1dvp_1#4  1       mfrssfck nlenatshlr lepdwpsill icdeinqkdv tpknafaaik
                                                                      
TARGET                 hhh hhhhhh         hhhhhh hhhhhh      hhhhhhhhh
1dvp_1#4              hhhh hhhhhh         hhhhhh hhhhhhh     hhhhhhhhh


TARGET    49    KKMNSPNPHS SCYSLLVLES IVKNCGAPVH EEVFTKENCE MFSSFLESTP
1dvp_1#4  49    kkmnspnphs scysllvles ivkncgapvh eevftkence mfssflestp
                                                                      
TARGET          hhh    hhh hhhhhhhhhh hhh   hhhh hh   hhhhh hhhhhhh   
1dvp_1#4        hhh    hhh hhhhhhhhhh hh   hhhhh hh   hhhhh hhhhhhh   


TARGET    99    HENVRQKMLE LVQTWAYAFR SSDKYQAIKD TMTILKAKGH TFPELREADA
1dvp_1#4  99    henvrqkmle lvqtwayafr ssdkyqaikd tmtilkakgh tfpelre---
                                                                      
TARGET           hhhhhhhhh hhhhhhhh         hhhh hhhhhhh              
1dvp_1#4         hhhhhhhhh hhhhhhhh         hhhh hhhhhhh              


TARGET    149   MFTADTAPNW ADGRVCHRCR VEFTFTNRKH HCRNCGQVFC GQCTAKQCPL
1dvp_1#4  149   mftadtapnw adgrvchrcr veftftnrkh hcrncgqvfc gqctakqcpl
                                                                      
TARGET                        sss     sss      s ss    sss       sss  
1dvp_1#4                      sss     sss      s ss    sss       sss  


TARGET    199   PKYGIEKEVR VCDGCFAALQ R -- MFRSS FDKNLENATS HLRLEPDWPS
1dvp_1#4  199   pkygiekevr vcdgcfaalq r-g--mfrss fcknlenats hlrlepdwps
                                         *                            
TARGET                  ss s hhhhhhhh          h hhhhhhhh          hhh
1dvp_1#4                ss s hhhhhhhh          h hhhhhhhhh         hhh


TARGET    245   ILLICDEINQ KDVTPKNAFA AIKKKMNSPN PHSSCYSLLV LESIVKNCGA
1dvp_1#4  26    illicdeinq kdvtpknafa aikkkmnspn phsscysllv lesivkncga
                                                                      
TARGET          hhhhhhhhh      hhhhhh hhhhhh     hhhhhhhhhh hhhhhh   h
1dvp_1#4        hhhhhhhhhh     hhhhhh hhhhhh     hhhhhhhhhh hhhhh   hh


TARGET    295   PVHEEVFTKE NCEMFSSFLE STPHENVRQK MLELVQTWAY AFRSSDKYQA
1dvp_1#4  76    pvheevftke ncemfssfle stphenvrqk mlelvqtway afrssdkyqa
                                                                      
TARGET          hhhhh   hh hhhhhhhhhh     hhhhhh hhhhhhhhhh h        h
1dvp_1#4        hhhhh   hh hhhhhhhhhh     hhhhhh hhhhhhhhhh h        h


TARGET    345   IKDTMTILKA KGHTFPELRE ADAMFTADTA PNWADGRVCH RCRVEFTFTN
1dvp_1#4  126   ikdtmtilka kghtfpelre ---mftadta pnwadgrvch rcrveftftn
                                                                      
TARGET          hhhhhhhhhh                             sss     sss    
1dvp_1#4        hhhhhhhhhh                             sss     sss    


TARGET    395   RKHHCRNCGQ VFCGQCTAKQ CPLPKYGIEK EVRVCDGCFA ALQR      
1dvp_1#4  176   rkhhcrncgq vfcgqctakq cplpkygiek evrvcdgcfa alqrg     
                                                                      
TARGET            sss    s ss      ss s           sss hhhhh hhh       
1dvp_1#4          sss    s ss      ss s           sss hhhhh hhh

Quality 


Template's ligands section 
Ligands in the template: CIT: 2, MET: 2, ZN: 4. 
Ligands in the template that will be assessed: ZN1, ZN2, ZN241, ZN242. 
Model's ligands section 
ZN1 
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: 0.050 
Given the properties calculated previously, the ligand z.ZN1 will be included in the final model. 
ZN1: conservation:True, RMSD:True, included: True 
 
ZN2 
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: 0.050 
Given the properties calculated previously, the ligand z.ZN2 will be included in the final model. 
ZN2: conservation:True, RMSD:True, included: True 
 
ZN241 
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 z.ZN241 will be included in the final model. 
ZN241: conservation:True, RMSD:True, included: True 
 
ZN242 
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: 0.040 
Given the properties calculated previously, the ligand z.ZN242 will be included in the final model. 
ZN242: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 1dvp is annotated as 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: 1dvp.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=DIMER) 
 The corresponding reliability score is 0.728 (>0.5 indicates similarity) 
 Model was succesfully built as DIMER.

Template Selection 
 - Start SMR-Pipeline for:edb38649418e4b98480e70434667e42a on BC2-cluster at Fri Feb 22 13:20:51
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 D found
 - No template with C found
 - No template with F found
 - No template with F found
 - No template with E found
 - No template with G found
 - No template with A found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with E found
 - No template with F found
 - No template with D found
 - No template with C found
 - No template with S found
 - No template with C found
 - No template with C found
 - No template with C found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 - ***********************
 - building model based on 1dvpA (1-219) was successful 
 -                                         **********
 - building model based on 3f1iH (376-471) 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:edb38649418e4b98480e70434667e42a on BC2-cluster at Fri Feb 22 13:23:36
2013


Template Description
Match Chain SeqId

1dvp: CRYSTAL STRUCTURE OF THE VHS AND FYVE TANDEM DOMAINS OF HRA PROTEIN INVOLVED IN MEMBRANE TRAFFICKING AND SIGNAL TRANSDUCTION
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-219 1dvpA 98%
[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.