SWISS-MODEL Repository

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

Quaternary Structure Annotation of the Template 
 2dm4 is annotated as MONOMER 
 The template structure (2dm4) was solved by NMR and does not contain any quaternary structure annotation 
 The template is annotated by the number of chains found in the PDB file 
      
 
Quaternary Structure Modelling of the Target Protein 
 The quaternary structure can be assumed to be identical 
 Model was succesfully built as MONOMER.

 - Start SMR-Pipeline for:0927b7bf0eabe21da4ea2a2b2ad695e0 on BC2-cluster at Fri Feb 15 21:53:31
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  3
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Warning: sequence length exceeded the limit of 1500 residues
 - HHsearch profile build is skipped
FATAL - No A3m found

 - No template with A found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                             ***
 - building model based on 2dm4A (1651-1745) was successful 
 -                                           *
 - Oligomeric modeling of 1ajjA was not successful, fall back to monomeric modeling
 - building model based on 1ajjA (1158-1192) was not successful go to next best template
 -                                           *
 - building model based on 1j8eA (1156-1193) was successful 
 -                                            *
 - building model based on 2kriB (1198-1235) was not successful go to next best template
 - 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:0927b7bf0eabe21da4ea2a2b2ad695e0 on BC2-cluster at Fri Feb 15 21:54:08
2013