SWISS-MODEL Repository

Template's ligands section 
Ligands in the template: 3BI: 2, BMA: 2, CA: 2, CL: 2, MAN: 2, NAG: 20, ZN: 4. 
Ligands in the template that will be assessed: BMA11, BMA738, CA15, CA742, MAN12, MAN739, NAG1, NAG10, NAG2, NAG3, NAG4, NAG5, NAG6, NAG7, NAG728, NAG729, NAG730, NAG731, NAG732, NAG733, NAG734, NAG735, NAG736, NAG737, NAG8, NAG9, ZN13, ZN14, ZN740, ZN741. 
Model's ligands section 
NAG1 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG1 will not be included in the model. 
NAG1: conservation:False, RMSD:False, included: False 
 
NAG2 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG2 will not be included in the model. 
NAG2: conservation:False, RMSD:False, included: False 
 
NAG3 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG3 will not be included in the model. 
NAG3: conservation:False, RMSD:False, included: False 
 
NAG4 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG4 will not be included in the model. 
NAG4: conservation:False, RMSD:False, included: False 
 
NAG5 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG5 will not be included in the model. 
NAG5: conservation:False, RMSD:False, included: False 
 
NAG6 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG6 will not be included in the model. 
NAG6: conservation:False, RMSD:False, included: False 
 
NAG7 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG7 will not be included in the model. 
NAG7: conservation:False, RMSD:False, included: False 
 
NAG8 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG8 will not be included in the model. 
NAG8: conservation:False, RMSD:False, included: False 
 
NAG9 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG9 will not be included in the model. 
NAG9: conservation:False, RMSD:False, included: False 
 
NAG10 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG10 will not be included in the model. 
NAG10: conservation:False, RMSD:False, included: False 
 
BMA11 
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 z.BMA11 will be included in the model. 
BMA11: conservation:True, RMSD:True, included: True 
 
MAN12 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MAN12 will not be included in the model. 
MAN12: conservation:False, RMSD:False, included: False 
 
NAG728 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG728 will not be included in the model. 
NAG728: conservation:False, RMSD:False, included: False 
 
NAG729 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG729 will not be included in the model. 
NAG729: conservation:False, RMSD:False, included: False 
 
NAG730 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG730 will not be included in the model. 
NAG730: conservation:False, RMSD:False, included: False 
 
NAG731 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG731 will not be included in the model. 
NAG731: conservation:False, RMSD:False, included: False 
 
NAG732 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG732 will not be included in the model. 
NAG732: conservation:False, RMSD:False, included: False 
 
NAG733 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG733 will not be included in the model. 
NAG733: conservation:False, RMSD:False, included: False 
 
NAG734 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG734 will not be included in the model. 
NAG734: conservation:False, RMSD:False, included: False 
 
NAG735 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG735 will not be included in the model. 
NAG735: conservation:False, RMSD:False, included: False 
 
NAG736 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG736 will not be included in the model. 
NAG736: conservation:False, RMSD:False, included: False 
 
NAG737 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG737 will not be included in the model. 
NAG737: conservation:False, RMSD:False, included: False 
 
BMA738 
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 z.BMA738 will be included in the model. 
BMA738: conservation:True, RMSD:True, included: True 
 
MAN739 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.MAN739 will not be included in the model. 
MAN739: conservation:False, RMSD:False, included: False 
 
ZN13 
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 z.ZN13 will be included in the final model. 
ZN13: conservation:True, RMSD:True, included: True 
 
ZN14 
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 z.ZN14 will be included in the final model. 
ZN14: conservation:True, RMSD:True, included: True 
 
CA15 
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: 0.030 
Given the properties calculated previously, the ligand z.CA15 will be included in the final model. 
CA15: conservation:True, RMSD:True, included: True 
 
ZN740 
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 z.ZN740 will be included in the final model. 
ZN740: conservation:True, RMSD:True, included: True 
 
ZN741 
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 z.ZN741 will be included in the final model. 
ZN741: conservation:True, RMSD:True, included: True 
 
CA742 
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 z.CA742 will be included in the final model. 
CA742: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

Quaternary Structure Annotation of the Template 
 3bi1 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: 3bi1.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 0.936 (>0.5 indicates similarity) 
 Model was succesfully built as DIMER.

 - Start SMR-Pipeline for:1e01b07aa4f48c00fc94d53e08363480 on BC2-cluster at Sat Feb 16 21:41:33
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

FATAL - 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 A found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with G found
 - No template with H found
 - No template with G found
 - No template with H found
 - No template with D found
 - No template with D found
 - No template with C found
 - No template with C found
 - No template with D found
 - No template with D found
 - No template with C found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with D found
 - No template with D found
 - No template with C found
 - No template with C 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 3bi1A (61-752) 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:1e01b07aa4f48c00fc94d53e08363480 on BC2-cluster at Sat Feb 16 23:54:43
2013