SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: ALA: 2, GOL: 5, MN: 1, PO4: 1, SO4: 3. 
Ligands in the template that will be assessed: MN463. 
Model's ligands section 
MN463 
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: 0.060 
Given the properties calculated previously, the ligand B.MN463 will be included in the final model. 
MN463: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 3rzi is annotated as TETRAMER 
 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: 3rzi.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 (=TETRAMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.118 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 3rziA 

 - Start SMR-Pipeline for:b9ad6eede1f159ce8c1e2f5161a2c301 on BC2-cluster at Sun May  5 01:43:53
2013 


 - 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 modified template library 
 - Summarize templates: 
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D 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 3rziA (83-515) was not successful go to next best template
 -              ******************************************************************
 - building model based on 3rziB (83-515) 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:b9ad6eede1f159ce8c1e2f5161a2c301 on BC2-cluster at Sun May  5 01:57:08
2013