SWISS-MODEL Repository - Model Details

Model Overview
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1
196

Sequence
UniProt P06850
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P06850: 9606.ENSP0000027

Domain
Link to: [ InterPro ]
CRF

Model 3D Structure
Model information:
Modelled residue range: 154 to 194
Based on template: [ 1go9 ]  
Sequence Identity [%]: 92%
Model date: 2014-09-19
Revision date: 2014-09-17

Quaternary structure information: [details]
Template (1go9): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ALA: 1, NH2: 1.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

TARGET    1       SEEPPISL DLTFHLLREV LEMARAEQLA QQAHSNRKLM EII       
1go9A     1       seeppisl dlth--lrev lemaraeqla qqahsnrklm eii-      
                                                                      
TARGET                 hhh hhhh        hhhhhhhhh    hhhhhhh hh        
1go9A                  hhh hh          hhhhhhhhh    hhhhhhh hh        



Quality


Template's ligands section
Ligands in the template: ALA: 1, NH2: 1.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.


Quaternary Structure Annotation of the Template
1go9 is annotated as MONOMER
The template structure (1go9) 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
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 0.192 (>0.5 indicates similarity)


Template Selection
 - Start SMR-Pipeline for:7b1efb02aea107aeb46b16cf20e749cf on BC2-cluster at Fri Sep 19 18:38:01
2014 


 - 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

 - No A3m found

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange - make sure all DBs are sync'ed correctly
 - 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 1go9A (154-194) 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:7b1efb02aea107aeb46b16cf20e749cf on BC2-cluster at Fri Sep 19 18:38:50
2014 




Template Description
Match Chain SeqId

1goe: MONITORING THE STRUCTURAL CONSEQUENCES OF PHE12-->D-PHE12 AND LEU15-->AIB15 SUBSTITUTION IN H/R CORTICOTROPIN RELEASING HORMONE: IMPLICATIONS FOR DESIGN OF CRH ANTAGONISTS.
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

154-194 1goeA 93%
[Model]

1go9: MONITORING THE STRUCTURAL CONSEQUENCES OF PHE12-->D-PHE12 AND LEU15-->AIB15 SUBSTITUTION IN H/R CORTICOTROPIN RELEASING HORMONE: IMPLICATIONS FOR DESIGN OF CRH ANTAGONISTS.
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

154-194 1go9A 93%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.




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