SWISS-MODEL Repository - Model Details

Model Overview
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1
1120

Sequence
UniProt P76072
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P76072: 511145.b1372

Domain
Link to: [ InterPro ]
Phage_fiber
Phage_fiber
Phage_fiber
Phage_fiber
Phage_fiber
Phage_fiber
Phage_fiber
Collar
phage_tail_N

Model 3D Structure
Model information:
Modelled residue range: 903 to 1120
Based on template: [ 2xgf ]  
Sequence Identity [%]: 69%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2xgf): TRIMER
Model: TRIMER

Ligand information: [details]
Ligands in the template: CO3: 1, FE2: 7.
Ligands in the model: FE2: 7
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-01-30. 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 

TARGET    1        SYPVGAP IPWPSDTVPS GYALMQGQAF DKSAYPKLAA AYPSGVIPDM
2xgf_1#9  811   s--sypigap ipwpsdsvpa gfalmegqtf dksaypklav aypsgvipdm
                                                                      
TARGET                     sss        sssss  sss      hhhhh h   sss   
2xgf_1#9                   sss        sssss  sss      hhhhh h   sss   


TARGET    48    RGWTIKGKPA SGRAVLSQEQ DGIKSHTHSA SASSTDLGTK TTSSFDYGTK
2xgf_1#9  859   rgqtikgkp- sgravlsaea dgvkahshsa sasstdlgtk ttssfdygtk
                                                                      
TARGET             sssss         sss          ss sss ssssss ss  ssssss
2xgf_1#9           sssss         sss          ss sss ssssss ss  ssssss


TARGET    98    STNNTGAHTH SVSGSTNSAG AHTHSLANVN TASANSGAGS ASTRLSVVHN
2xgf_1#9  908   gtnstgghth sgsgststng ehshyieawn gtgv--ggnk mssyaisyra
                                                                      
TARGET          ss       s ssssss        sssssss s                ssss
2xgf_1#9        ss       s ssssss        sssssss s                ssss


TARGET    148   QNYATSSAGA HTHSLSGTAA SAGAHAHTVG IGAHTHSVAI GSHGHTITVN
2xgf_1#9  956   ggsntnaagn hshtfsfgts sagdhshsvg igahthtvai gshghtitvn
                                                                      
TARGET          sssss        sssssss        ssss ssss sssss sss  sssss
2xgf_1#9        sssss        sssssss        ssss ssss sssss sss  sssss


TARGET    198   AAGNAENTVK NIAFNYIVRL A -- SYPVG APIPWPSDTV PSGYALMQGQ
2xgf_1#9  1006  stgntentvk niafnyivrl a-s--sypig apipwpsdsv pagfalmegq
                                         *                            
TARGET                   s ssssssssss              sss        sssss  s
2xgf_1#9                 s ssssssssss              sss        sssss  s


TARGET    244   AFDKSAYPKL AAAYPSGVIP DMRGWTIKGK PASGRAVLSQ EQDGIKSHTH
2xgf_1#9  837   tfdksaypkl avaypsgvip dmrgqtikgk p-sgravlsa eadgvkahsh
                                                                      
TARGET          ss     hhh hhh   sss       sssss         ss s         
2xgf_1#9        ss     hhh hhh   sss       sssss         ss s         


TARGET    294   SASASSTDLG TKTTSSFDYG TKSTNNTGAH THSVSGSTNS AGAHTHSLAN
2xgf_1#9  886   sasasstdlg tkttssfdyg tkgtnstggh thsgsgstst ngehshyiea
                                                                      
TARGET          sssss ssss ssss  ssss ssss        sssssss        sssss
2xgf_1#9        sssss ssss ssss  ssss ssss        sssssss        sssss


TARGET    344   VNTASANSGA GSASTRLSVV HNQNYATSSA GAHTHSLSGT AASAGAHAHT
2xgf_1#9  936   wngtgv--gg nkmssyaisy raggsntnaa gnhshtfsfg tssagdhshs
                                                                      
TARGET          sss                ss sssssss        ssssss s       ss
2xgf_1#9        sss                ss sssssss        ssssss s       ss


TARGET    394   VGIGAHTHSV AIGSHGHTIT VNAAGNAENT VKNIAFNYIV RLA -- SYP
2xgf_1#9  984   vgigahthtv aigshghtit vnstgntent vkniafnyiv rla-s--syp
                                                                 *    
TARGET          ssssss sss sssss  sss ss          sssssssss ss        
2xgf_1#9        ssssss sss sssss  sss ss          sssssssss ss        


TARGET    440   VGAPIPWPSD TVPSGYALMQ GQAFDKSAYP KLAAAYPSGV IPDMRGWTIK
2xgf_1#9  815   igapipwpsd svpagfalme gqtfdksayp klavaypsgv ipdmrgqtik
                                                                      
TARGET              sss        sssss   sss     h hhhhh   ss s      sss
2xgf_1#9            sss        sssss   sss     h hhhhh   ss s      sss


TARGET    490   GKPASGRAVL SQEQDGIKSH THSASASSTD LGTKTTSSFD YGTKSTNNTG
2xgf_1#9  865   gkp-sgravl saeadgvkah shsasasstd lgtkttssfd ygtkgtnstg
                                                                      
TARGET          ss         sss          sssss ss ssssss  ss ssssss    
2xgf_1#9        ss         sss          sssss ss ssssss  ss ssssss    


TARGET    540   AHTHSVSGST NSAGAHTHSL ANVNTASANS GAGSASTRLS VVHNQNYATS
2xgf_1#9  914   ghthsgsgst stngehshyi eawngtgv-- ggnkmssyai syraggsntn
                                                                      
TARGET             sssssss        sss sssss                 sssssssss 
2xgf_1#9           sssssss        sss sssss                 sssssssss 


TARGET    590   SAGAHTHSLS GTAASAGAHA HTVGIGAHTH SVAIGSHGHT ITVNAAGNAE
2xgf_1#9  962   aagnhshtfs fgtssagdhs hsvgigahth tvaigshght itvnstgnte
                                                                      
TARGET                ssss sss        ssssssss s sssssss  s ssss      
2xgf_1#9              ssss sss        ssssssss s sssssss  s ssss      


TARGET    640   NTVKNIAFNY IVRLA                                      
2xgf_1#9  1012  ntvkniafny ivrla-                                     
                                                                      
TARGET             sssssss ssss                                       
2xgf_1#9           sssssss ssss

Quality 


Template's ligands section 
Ligands in the template: CO3: 1, FE2: 7. 
Ligands in the template that will be assessed: FE21, FE22, FE23, FE24, FE25, FE26, FE27. 
Model's ligands section 
FE21 
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: 0.050 
Given the properties calculated previously, the ligand z.FE21 will be included in the final model. 
FE21: conservation:True, RMSD:True, included: True 
 
FE22 
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.FE22 will be included in the final model. 
FE22: conservation:True, RMSD:True, included: True 
 
FE23 
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 z.FE23 will be included in the final model. 
FE23: conservation:True, RMSD:True, included: True 
 
FE24 
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: 0.050 
Given the properties calculated previously, the ligand z.FE24 will be included in the final model. 
FE24: conservation:True, RMSD:True, included: True 
 
FE25 
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: 0.070 
Given the properties calculated previously, the ligand z.FE25 will be included in the final model. 
FE25: conservation:True, RMSD:True, included: True 
 
FE26 
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: 0.070 
Given the properties calculated previously, the ligand z.FE26 will be included in the final model. 
FE26: conservation:True, RMSD:True, included: True 
 
FE27 
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: 0.050 
Given the properties calculated previously, the ligand z.FE27 will be included in the final model. 
FE27: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 2xgf is annotated as TRIMER 
 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: 2xgf.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The quaternary structure can be assumed to be identical 
 To build the complex the following chains of the complex has been additionally identified: 2xgfC 2xgfB  
 Model was succesfully built as TRIMER.

Template Selection 
 - Start SMR-Pipeline for:412e38a19b32c016350f8e9b06e14262 on BC2-cluster at Sat Feb 23 08:43:32
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...
FATAL - No templates found in HHSEARCH, strange
 - 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 2xgfA (903-1120) 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:412e38a19b32c016350f8e9b06e14262 on BC2-cluster at Sat Feb 23 08:46:34
2013


Template Description
Match Chain SeqId

2xgf: STRUCTURE OF THE BACTERIOPHAGE T4 LONG TAIL FIBRE NEEDLE- SHAPED RECEPTOR-BINDING TIP
Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

903-1120 2xgfA 69%
[Model]
903-1120 2xgfC 69%
[Model]
903-1120 2xgfB 69%
[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.