SWISS-MODEL Repository - Model Details

Model Overview
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1
151

Sequence
UniProt Q9VLJ0
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9VLJ0: 7227.FBpp0079352

Domain
Link to: [ InterPro ]
GMP_PDE_delta

Model 3D Structure
Model information:
Modelled residue range: 12 to 151
Based on template: [ 3t5i ]  
Sequence Identity [%]: 64%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3t5i): 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                 IQKGFQINY MILRDADSGK IIWQENKDFS APDQEHEARV
3t5iA     2     sakderare- -ilrgfklnw mnlrdaetgk ilwqgtedls vpgvehearv
                                                                      
TARGET                         ssssss ssssss   s sssss           sssss
3t5iA            hhhhhhhh   hhhssssss ssssss   s sssss           sssss


TARGET    40    PVKILDMRAV SREINFSTIE SMENFRLDQK VLFKGRIMEE WFFEMGFVGA
3t5iA     50    pkkilkckav srelnfsste qmekfrleqk vyfkgqclee wffefgfvip
                                                                      
TARGET          sshhh   ss sssssssss     sssssss ssss sssss sssss     
3t5iA           sshhh   ss sssssssss     sssssss ssss sssss sssss     


TARGET    90    NTTNTWQSTI EAAPESQMMP AKVLNGNVTI QTSFYDNETL ITKSVVRLYY
3t5iA     100   nstntwqsli eaapesqmmp asvltgnvii etkffdddll vstsrvrlfy
                                                                      
TARGET          ssssssss              hhhh  ssss sssssss ss ssssssssss
3t5iA           ssssssss              hhhh  ssss sssssss ss ssssssssss


TARGET    140   I                                                     
3t5iA     150   v-                                                    
                                                                      
TARGET          s                                                     
3t5iA           s

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3t5i 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: 3t5i.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 0.34 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:17610e407d55d7e04f7ebdb947902d7b on BC2-cluster at Thu Feb 21 14:53:16
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 3t5iA (12-151) 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:17610e407d55d7e04f7ebdb947902d7b on BC2-cluster at Thu Feb 21 14:54:12
2013


Template Description
Match Chain SeqId

3t5g: STRUCTURE OF FULLY MODIFIED FARNESYLATED RHEB IN COMPLEX W
Solved by: X-RAY, Resolution: 1.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

12-151 3t5gB 64%
[Model]

3t5i: STRUCTURE OF FULLY MODIFIED FARNESYLATED RHEB PEPTIDE IN CPDE6D
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

12-151 3t5iB 61%
[Model]
12-151 3t5iC 64%
[Model]
12-151 3t5iD 64%
[Model]
12-151 3t5iA 64%
[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.