SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: DTT: 1, ZN: 2. 
Ligands in the template that will be assessed: ZN400, ZN401. 
Model's ligands section 
ZN400 
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 D.ZN400 will be included in the final model. 
ZN400: conservation:True, RMSD:True, included: True 
 
ZN401 
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: 0.080 
Given the properties calculated previously, the ligand D.ZN401 will be included in the final model. 
ZN401: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 3k2g is annotated as MONOMER 
 PISA was used to annotate the quaternary structure, because the author assignment was ambigous (i.e the same chains appear in different biolgoical units annotated by the author) 
 PISA annotates this structure as Monomer, therefore the corresponding PDB chain was used as template structure 
      
 
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 0.294 (>0.5 indicates similarity)

 - Start SMR-Pipeline for:daec64aad29e1325beb7d183539764ec on BC2-cluster at Sat Apr 20 13:24:56
2013 


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

 - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with B 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 3k2gD (5-344) 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:daec64aad29e1325beb7d183539764ec on BC2-cluster at Sat Apr 20 13:47:48
2013