SWISS-MODEL Repository - Model Details

Model Overview
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1
417

Sequence
UniProt Q3TNH5
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Arb2

Model 3D Structure
Model information:
Modelled residue range: 116 to 328
Based on template: [ 3fnb ]  
Sequence Identity [%]: 8%
Model date: 2013-05-08
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (3fnb): DIMER
Model built: SINGLE CHAIN

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

Alignment 

                                                       
3fnbB     11    qdykikfnnk dxdfcfnwxl gigqiigxsa gelfyiasgi rdgnptdwck
                                                                      
                                                       
3fnbB                    h hhhhhhhhhh hhhhh    h hhhhhhhh       hhhhhh


                                                       
3fnbB     61    rfnehadyle devervkkvg yrdlishlyf sacfsiraal qftdpkdsef
                                                                      
                                                       
3fnbB           hhhhhhhhhh hhhhhhh     hhhhhhhhh hhhhhhhhhh         hh


TARGET    1                           DCNLKKISIP VDATESEPKS FIFMSEDALT
3fnbB     112   xenfrrxekl fxlavdns-- kiplksievp fegel--lpg y-aiise--d
                                                                      
TARGET                                  sssssss         sss ssss      
3fnbB           hhhhhhhhhh hhhhhhh        ssssss s  ss  sss s ss      


TARGET    31    NPQKLMVLIH GSGVVRAGQW ARRLIINEDL DSGTQIPFIK RAMDEGYGVI
3fnbB     154   kaqdtlivvg ggdtsredl- ---------- ----fyxlgy sgwehdynvl
                                                                      
TARGET             sssssss s                             hh hhhh   sss
3fnbB              sssssss s    hhhh                 hh   h hhhh   sss


TARGET    81    VLNPN-ENYI EVEKQKMHKQ SSSSDGTDEP AGKRERRDKV SKETKKRRDF
3fnbB     190   xvdlpgq--- --------g- -kn------- ---------- ------pn--
                                                                      
TARGET          ssshh hhhh hhh                         hhhh hhhhhhhhhh
3fnbB           sss                     h                         h   


TARGET    130   YEKYRNPQKE KEMMQLFIRE NGSPEEHAVY VWDHFIAQAA AENVFFVAHS
3fnbB     201   -------q-- ------glhf evdaraaisa ildwy--qap tekiaiagfs
                                                                      
TARGET          hh    hhhh hhh            hhhhhh hhhh         ssssssss
3fnbB                                     hhhhhh hhhh         ssssssss


TARGET    180   YGGLAFVELM IQREADVKSK VTAVALTDSV HNVW ----- ----------
3fnbB     234   gggyftaqav ekd-----kr ikawiastpi ydvaevfris fsvnkvaevn
                                                                      
TARGET           hhhhhhhhh              sssss                         
3fnbB            hhhhhhhhh hh           sssss       hhhhhhh     hhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
3fnbB     298   lnkyawqfgq vdfitsvnev leqaqivdyn kidvpslflv gagedselxr
                                                                      
TARGET                                                                
3fnbB           hhhhhhhh     hhhhhhhh hhh            ssssss ss   hhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
3fnbB     348   qsqvlydnfk qrgidvtlrk fssesgadah cqvnnfrlxh yqvfewlnhi
                                                                      
TARGET                                                                
3fnbB           hhhhhhhhhh hh  ssssss s                hhhh hhhhhhhhhh


TARGET          ---                                                   
3fnbB     398   fkk                                                   
                                                                      
TARGET                                                                
3fnbB           h

Quality 


Template's ligands section 
Ligands in the template: BME: 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 
 3fnb 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: 3fnb.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The target and template sequences are too diverse (seqid: 8.879) 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 
 To build the complex the following chains of the complex has been additionally identified: 3fnbA

Template Selection 
 - Start SMR-Pipeline for:d977c764758a1ff5036bb689847dc536 on BC2-cluster at Wed May  8 03:16:45
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - 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:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                       *****************************************
 - building model based on 3fnbA (116-328) was not successful go to next best template
 -                       *****************************************
 - building model based on 3fnbB (116-328) 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:d977c764758a1ff5036bb689847dc536 on BC2-cluster at Wed May  8 03:27:23
2013


Template Description
Match Chain SeqId

3fnb: CRYSTAL STRUCTURE OF ACYLAMINOACYL PEPTIDASE SMU_737 FROM STREPTOCOCCUS MUTANS UA159
Solved by: X-RAY, Resolution: 2.12A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

116-328 3fnbA 9%
[Model]
116-328 3fnbB 9%
[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.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.