SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: A3P: 6, CL: 6, MG: 9. 
Ligands in the template that will be assessed: MG1, MG185, MG186, MG188, MG2, MG4, MG96, MG97, MG99. 
Model's ligands section 
MG1 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG1 will not be included in the final model. 
MG1: conservation:False, RMSD:False, included: False 
 
MG2 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG2 will not be included in the final model. 
MG2: conservation:False, RMSD:False, included: False 
 
MG4 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG4 will not be included in the final model. 
MG4: conservation:False, RMSD:False, included: False 
 
MG96 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG96 will not be included in the final model. 
MG96: conservation:False, RMSD:False, included: False 
 
MG97 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG97 will not be included in the final model. 
MG97: conservation:False, RMSD:False, included: False 
 
MG99 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG99 will not be included in the final model. 
MG99: conservation:False, RMSD:False, included: False 
 
MG185 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG185 will not be included in the final model. 
MG185: conservation:False, RMSD:False, included: False 
 
MG186 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG186 will not be included in the final model. 
MG186: conservation:False, RMSD:False, included: False 
 
MG188 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MG188 will not be included in the final model. 
MG188: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

Quaternary Structure Annotation of the Template 
 3hyk is annotated as TRIMER 
 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: 3hyk.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 (=TRIMER) 
 The corresponding reliability score is 0.604 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 3hykA 3hykB  
 Model was succesfully built as TRIMER.

 - Start SMR-Pipeline for:ca785a79ffca371cf55e16477a38c60c on BC2-cluster at Wed Oct 31 21:17:32
2012 


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

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with B found
 - No template with B found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with G found
 - No template with J found
 - No template with I found
 - No template with H found
 - No template with L found
 - No template with K found
 - Proof template(s) selection compared to previous Repository update
 - Need for modeling since selected templates are the not the same as in previous update

 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -      ***************************************************************************
 - building model based on 3hykC (10-172) 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:ca785a79ffca371cf55e16477a38c60c on BC2-cluster at Wed Oct 31 21:25:45
2012