SWISS-MODEL Repository - Model Details

Model Overview
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1
164

Sequence
UniProt Q50604
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
DNase-RNase

Model 3D Structure
Model information:
Modelled residue range: 1 to 124
Based on template: [ 1vjl ]  
Sequence Identity [%]: 35%
Model date: 2013-02-13
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1vjl): DIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: CL: 1, UNL: 1.
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        MGEVRVV GIRVEQPQNQ PVLLLREANG DRYLPIWIGQ SEAAAIALEQ
1vjlA     0     h--xrkawvk tlaldrvsnt pvvilgiegt nrvlpiwiga ceghalalax
                                                                      
TARGET              ssssss sssss    s ssssssss    sssssss h hhhhhhhhhh
1vjlA           s  sssssss sssss    s ssssssss   ssssssss h hhhhhhhhhh


TARGET    48    QGVEPPRPLT HDLIRDLIAA LGHSLKEVRI VDLQEGTFYA DLIFDR----
1vjlA     48    ekxefprplt hdlllsvles learvdkvii hslkdntfya tlvirdltaa
                                                                      
TARGET          h        h hhhhhhhhhh h  sssssss ssss  ssss sssss     
1vjlA           h        h hhhhhhhhhh hsssssssss ssss  ssss sssssss  s


TARGET    94    NIKVSARPSD SVAIALRVGV PIYVEEAVLA Q -------- -----     
1vjlA     106   lididsrpsd aiilavktga pifvsdnlve khsielevne rdlin     
                                                                      
TARGET           sssss hhh hhhhhhhh   ssssshhhhh h                    
1vjlA           ssssss hhh hhhhhhhh   sssssshhhh h  sss hhh hhhh

Quality 


Template's ligands section 
Ligands in the template: CL: 1, UNL: 1. 
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 1vjl 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: 1vjl.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 (=DIMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.228 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 1vjlB

Template Selection 
 - Start SMR-Pipeline for:b3a95aaa73e3242357bd95cf1c92d1d8 on BC2-cluster at Wed Feb 13 05:12:48
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

FATAL - No A3m found

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - 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 1vjlA (1-124) 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:b3a95aaa73e3242357bd95cf1c92d1d8 on BC2-cluster at Wed Feb 13 05:21:00
2013

no data available!
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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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