SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: CA: 1, MG: 1, NAG: 2, PNP: 2, PO3: 1, ZN: 2. 
Ligands in the template that will be assessed: CA906, MG905, NAG801, NAG803, ZN903, ZN904. 
Model's ligands section 
NAG801 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand NAG801 will not be included in the model. 
NAG801: conservation:False, RMSD:False, included: False 
 
NAG803 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand NAG803 will not be included in the model. 
NAG803: conservation:False, RMSD:False, included: False 
 
ZN903 
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 ZN903 will be included in the final model. 
ZN903: conservation:True, RMSD:True, included: True 
 
ZN904 
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 ZN904 will be included in the final model. 
ZN904: conservation:True, RMSD:True, included: True 
 
MG905 
Not all the residues interacting with the ligand are completely conserved between model and template. 
No RMSD calculation will be performed. 
Given the properties calculated previously, the ligand MG905 will not be included in the final model. 
MG905: conservation:False, RMSD:False, included: False 
 
CA906 
Not all the residues interacting with the ligand are completely conserved between model and template. 
No RMSD calculation will be performed. 
Given the properties calculated previously, the ligand CA906 will not be included in the final model. 
CA906: conservation:False, RMSD:False, included: False 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 1zed 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: 1zed.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 (=DIMER) 
 The corresponding reliability score is 0.72 (>0.5 indicates similarity) 
 Unfortunately, we were not able to built the model as DIMER. 
 Thus, the model was built as single chain.

 - Start SMR-Pipeline for:5c121ddc6c657edb54facee2c3deb243 on BC2-cluster at Thu Feb 21 10:35:28
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...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -        ******************************************************************
 - Oligomeric modeling of 1zedA was not successful, fall back to monomeric modeling
 - building model based on 1zedA (50-542) 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:5c121ddc6c657edb54facee2c3deb243 on BC2-cluster at Thu Feb 21 11:48:16
2013