SWISS-MODEL Repository - Model Details

Model Overview
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Sequence
UniProt P08F94
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P08F94: 9606.ENSP0000036

Domain
Link to: [ InterPro ]
TIG
TIG
TIG
TIG
TIG
TIG
TIG
G8
G8
Beta_helix
Beta_helix

Model 3D Structure
Model information:
Modelled residue range: 2230 to 2269
Based on template: [ 4nk8 ]  
Sequence Identity [%]: 24%
Model date: 2014-04-14
Revision date: 2014-04-08

Quaternary structure information: [details]
Template (4nk8): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ALA: 2.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2014-04-08. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment

                                                       
4nk8A     69    emakpvlpdl sgytteaalk kiarnkpgki tvarmmeetg lefiggdnkm
                                                                      
                                                       
4nk8A                          hhhh           ss sssss                


                                                       
4nk8A     120   aewvvrqkgi pqaimisdgy vnlqdlvkkv pkqflsevsp gvyvarlpil
                                                                      
                                                       
4nk8A           hhhhhhh    sssssss ss ssshhhhhh     sssss   ssssss sss


                                                       
4nk8A     170   vketgifeid sktkelrlsq egsfivsegk mlitntsvna wsetrnglaa
                                                                      
                                                       
4nk8A           ss ssssss      ssssss    sssssss sssss ssss ss    sss 


                                                       
4nk8A     221   yrtpdefrpf vltwggsqtw iatkmasmgy nqssygvsis qytpntakvl
                                                                      
                                                       
4nk8A                    s sssss ssss sssssss         sssss s  hhhhhhh


TARGET    1                                      FIQGCTVRNS FSRGLSMCG-
4nk8A     273   krgeptgwii dsefadmwyg fycyetrd-- fvvgntyrdn ivygiaphdr
                                                                      
TARGET                                                          sss   
4nk8A                sssss  ssss      ssss       sss sssss      sssss 


TARGET    20    TLGLKVDSNV FYNILGHALL V -------- ---------- ----------
4nk8A     322   shgliiaend vygtkkhgii isrevdnsfi frnshnnkls gvvldrnsvg
                                                                      
TARGET                            sss                                 
4nk8A              sssss s ss     sss sss    sss ss sss     ssssss    


TARGET          ---------- ---------- ---------- ---------- ----------
4nk8A     374   nivayneiyq nhtdgitlye sgnnllwgnr vianrrhgir vrnsvnikly
                                                                      
TARGET                                                                
4nk8A           ssssssssss     ssssss    sssssss sss    sss ssssssssss


TARGET          ---------- ---------- ---------- ---------- ----------
4nk8A     424   envamanglm gvyghikdln dtdrdieldp fdaqvslimv ggelssngsg
                                                                      
TARGET                                                                
4nk8A           ssssss     sssss                    sssssss s sss     


TARGET          ---------- ---------                                  
4nk8A     474   plsidsplsv elyrvsmlm                                  
                                                                      
TARGET                                                                
4nk8A           sssss   ss sss                                        



Quality


Template's ligands section
Ligands in the template: ALA: 2.
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
4nk8 is annotated as MONOMER
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: 4nk8.pdb1.gz

Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 24.390) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode

The target structure was calculated as SINGLE CHAIN


Template Selection
 - Start SMR-Pipeline for:5184e3c25d6453985fe161a12d4fc113 on BC2-cluster at Mon Apr 14 16:50:11
2014 


 - 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 modified template library 
 - Summarize templates: 
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:11): model based on new templates
 - Send 11 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                             *
 - building model based on 4nk8A (2230-2269) was successful 
 -                                                            *
 - building model based on 4nk8A (3014-3066) was successful 
 -                                                            **
 - building model based on 4nk6A (3015-3132) was successful 
 -                                                            **
 - building model based on 4nk8A (2987-3106) was not successful go to next best template
 -                                                             ***
 - building model based on 4nk6A (3038-3180) was successful 
 -                                               *
 - building model based on 4nk6A (2360-2428) was successful 
 -                                                            ***
 - building model based on 4nk6A (3006-3161) was successful 
 -                                            ***
 - building model based on 4nk8A (2215-2377) was successful 
 -                                              ***
 - building model based on 4nk8A (2291-2435) was successful 
 -                                             ***
 - building model based on 4nk6A (2230-2404) was successful 
 -                                             ****
 - building model based on 4nk8A (2229-2431) 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:5184e3c25d6453985fe161a12d4fc113 on BC2-cluster at Mon Apr 14 16:57:19
2014 




Template Description
Match Chain SeqId

4nk8: CRYSTAL STRUCTURE OF THE PERIPLASMIC ALGINATE EPIMERASE ALMUTANT
Solved by: X-RAY, Resolution: 2.29A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2225-2269 4nk8A 20%
[Model]
3013-3180 4nk8A 15%
[Model]
3013-3134 4nk8A 17%
[Model]
3015-3107 4nk8A 18%
[Model]
3037-3180 4nk8A 14%
[Model]
2230-2269 4nk8A 24%
[Model]
3014-3066 4nk8A 22%
[Model]
2987-3106 4nk8A 17%
[Model]
2229-2431 4nk8A 13%
[Model]
2215-2377 4nk8A 15%
[Model]
2291-2435 4nk8A 15%
[Model]

4nk6: CRYSTAL STRUCTURE OF THE PERIPLASMIC ALGINATE EPIMERASE AL
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3012-3180 4nk6A 14%
[Model]
3006-3161 4nk6A 16%
[Model]
2360-2428 4nk6A 16%
[Model]
3038-3180 4nk6A 16%
[Model]
2230-2404 4nk6A 14%
[Model]
3015-3132 4nk6A 18%
[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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