SWISS-MODEL Repository - Model Details

Model Overview
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1
987

Sequence
UniProt P16861
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P16861: 4932.YGR240C

Domain
Link to: [ InterPro ]
PFK
PFK

Model 3D Structure
Model information:
Modelled residue range: 203 to 980
Based on template: [ 3o8o ]  
Sequence Identity [%]: 96%
Model date: 2013-02-19
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3o8o): HETERO TETRAMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: F6P: 2, FDP: 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 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       QKKKKIAV MTSGGDSPGM NAAVRAVVRT GIHFGCDVFA VYEGYEGLLR
3o8oE     203     qkkkkiav mtsggdspgm naavravvrt gihfgcdvfa vyegyegllr
                                                                      
TARGET               sssss s        h hhhhhhhhhh hhh   ssss ss  hhhhhh
3o8oE                sssss s        h hhhhhhhhhh hhh   ssss ss  hhhhhh


TARGET    49    GGKYLKKMAW EDVRGWLSEG GTLIGTARSM EFRKREGRRQ AAGNLISQGI
3o8oE     251   ggkylkkmaw edvrgwlseg gtligtarsm efrkregrrq aagnlisqgi
                                                                      
TARGET             sssss                         hh   hhhhh hhhhhhhh  
3o8oE              sssss                         hh   hhhhh hhhhhhhh  


TARGET    99    DALVVCGGDG SLTGADLFRH EWPSLVDELV AEGRFTKEEV APYKNLSIVG
3o8oE     301   dalvvcggdg sltgadlfrh ewpslvdelv aegrftkeev apyknlsivg
                                                                      
TARGET          sssssss hh hhhhhhhh    hhhhhhhhh       hh         ssss
3o8oE           sssssss hh hhhhhhhh    hhhhhhhhh       hh         ssss


TARGET    149   LVGSIDNDMS GTDSTIGAYS ALERICEMVD YIDATAKSHS RAFVVEVMGR
3o8oE     351   lvgsidndms gtdstigays alericemvd yidatakshs rafvvevmgr
                                                                      
TARGET          sss               hhh hhhhhhhhhh hhhhhhhhh  sssssss   
3o8oE           ssss            ssshh hhhhhhhhhh hhhhhhhhh  sssssss   


TARGET    199   HCGWLALMAG IATGADYIFI PERAVPHGKW QDELKEVCQR HRSKGRRNNT
3o8oE     401   hcgwlalmag iatgadyifi peravphgkw qdelkevcqr hrskgrrnnt
                                                                      
TARGET             hhhhhhh hhh   sss           h hhhhhhhhhh hhhh    ss
3o8oE              hhhhhhh hh    sss           h hhhhhhhhhh hhhh    ss


TARGET    249   IIVAEGALDD QLNPVTANDV KDALIELGLD TKVTILGHVQ RGGTAVAHDR
3o8oE     451   iivaegaldd qlnpvtandv kdalielgld tkvtilghvq rggtavahdr
                                                                      
TARGET          sssss sss    sss hhhh hhhhhhh  s ssssss  hh       hhhh
3o8oE           sssss sss    sss hhhh hhhhhhh  s ssss             hhhh


TARGET    299   WLATLQGVDA VKAVLEFTPE TPSPLIGILE NKIIRMPLVE SVKLTKSVAT
3o8oE     501   wlatlqgvda vkavleftpe tpspligile nkiirmplve svkltksvat
                                                                      
TARGET          hhhhhhhhhh hhhhhh       sssssss   ssssssshh hhhhhhhhhh
3o8oE           hhhhhhhhhh hhhhhh       sssssss   ssssssshh hhhhhhhhhh


TARGET    349   AIENKDFDKA ISLRDTEFIE LYENFLSTTV KDDGSELLPV SDRLNIGIVH
3o8oE     551   aienkdfdka islrdtefie lyenflsttv kddgsellpv sdrlnigivh
                                                                      
TARGET          hhh   hhhh hh    hhhh hhhhhhhh                 sssssss
3o8oE           hhh   hhhh hh    hhhh hhhhhhhh                 sssssss


TARGET    399   VGAPSAALNA ATRAATLYCL SHGHKPYAIM NGFSGLIQTG EVKELSWIDV
3o8oE     601   vgapsaalna atraatlycl shghkpyaim ngfsgliqtg evkelswidv
                                                                      
TARGET          s     hhhh hhhhhhhhhh hh  ssssss   hhhhhh   sssss  hh 
3o8oE           s      hhh hhhhhhhhhh hh  ssssss   hhhhhh   sssss  hh 


TARGET    449   ENWHNLGGSE IGTNRSVASE DLGTIAYYFQ KNKLDGLIIL GGFEGFRSLK
3o8oE     651   enwhnlggse igtnrsvase dlgtiayyfq knkldgliil ggfegfrslk
                                                                      
TARGET                                 hhhhhhhhh hh   sssss sshhhhhhhh
3o8oE                                  hhhhhhhhh hh   sssss sshhhhhhhh


TARGET    499   QLRDGRTQHP IFNIPMCLIP ATVSNNVPGT EYSLGVDTCL NALVNYTDDI
3o8oE     701   qlrdgrtqhp ifnipmclip atvsnnvpgt eyslgvdtcl nalvnytddi
                                                                      
TARGET          hhhhhhh    hh  ssssss s               hhhhh hhhhhhhhhh
3o8oE           hhhhhh   h hh  ssssss s               hhhhh hhhhhhhhhh


TARGET    549   KQSASATRRR VFVCEVQGGH SGYIASFTGL ITGAVSVYTP EKKIDLASIR
3o8oE     751   kqsasatrrr vfvcevqggh sgyiasftgl itgavsvytp ekkidlasir
                                                                      
TARGET          hhhhhhh ss ssssss       hhhhhhhh h    sss        hhhhh
3o8oE           hhhhhhh ss ssssss       hhhhhhhh h    sss        hhhhh


TARGET    599   EDITLLKENF RHDKGENRNG KLLVRNEQAS SVYSTQLLAD IISEASKGKF
3o8oE     801   editllkenf rhdkgenrng kllvrneqas svystqllad iiseaskgkf
                                                                      
TARGET          hhhhhhhhhh            sssssss        hhhhhh hhhhh     
3o8oE           hhhhhhhhhh h          sssssss        hhhhhh hhhhhh    


TARGET    649   GVRTAIPGHV QQGGVPSSKD RVTASRFAVK CIKFIEQWNK KNEASPNTDA
3o8oE     851   gvrtaipghv qqggvpsskd rvtasrfavk cikfieqwnk kne-------
                                                                      
TARGET          sssss    h h      hhh hhhhhhhhhh hhhhhhhhh    hhhhhhhh
3o8oE           sssss    h h      hhh hhhhhhhhhh hhhhhhhhhh h         


TARGET    699   KVLRFKFDTH GEKVPTVEHE DDSAAVICVN GSHVSFKPIA NLWENETNVE
3o8oE     920   ---------- ---------e ddsaavicvn gshvsfkpia nlwenetnve
                                                                      
TARGET          hhhhhhh               hh sssssss   sssssssh hh  sssss 
3o8oE                                   ssssssss   sssssssh hh  sssss 


TARGET    749   LRKGFEVHWA EYNKIGDILS GRLKLRAEVA                      
3o8oE     951   lrkgfevhwa eynkigdils grlklraeva -                    
                                                                      
TARGET          sssss      hhhhhhhh    hhhh                           
3o8oE           sssss      hhhhhhhh    hhhh

Quality 


Template's ligands section 
Ligands in the template: F6P: 2, FDP: 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 
 3o8o is annotated as HETERO TETRAMER 
 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: 3o8o.pdb2.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3o8o_2

Template Selection 
 - Start SMR-Pipeline for:4967961fe281934d849c24cdadc80cdb on BC2-cluster at Mon Feb 18 22:34:20
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

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with B found
 - No template with F found
 - No template with H found
 - No template with B found
 - No template with D found
 - No template with A found
 - No template with C found
 - No template with E found
 - No template with G found
 - No template with A found
 - No template with C found
 - No template with E found
 - No template with G found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with B found
 - No template with D found
 - No template with F found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with A found
 - No template with C found
 - No template with E found
 - No template with G found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                 ***************************************************************
 - building model based on 3o8oE (203-980) was successful 
 -  ******************************************************************************
 - building model based on 3opyE (10-976) 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:4967961fe281934d849c24cdadc80cdb on BC2-cluster at Mon Feb 18 23:12:37
2013


Template Description
Match Chain SeqId

3o8o: STRUCTURE OF PHOSPHOFRUCTOKINASE FROM SACCHAROMYCES CEREVI
Solved by: X-RAY, Resolution: 2.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

205-980 3o8oC 97%
[Model]
205-980 3o8oA 97%
[Model]
205-976 3o8oG 97%
[Model]
203-980 3o8oE 97%
[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.