SWISS-MODEL Repository - Model Details

Model Overview
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1
303

Sequence
UniProt P47968 Ribose-5-phosphate isomerase (Phosphoriboisomerase)
Mus musculus (Mouse).
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
P47968: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
Rib_5-P_isom_A

Model 3D Structure
Model information:
Modelled residue range: 72 to 301
Based on template: [ 1xtz ]  
Sequence Identity [%]: 47%
Model date: 2014-04-11
Revision date: 2014-04-08

Quaternary structure information: [details]
Template (1xtz): TETRAMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: none.
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

TARGET    1       EEAKKLAS HTAVENHVK- -NNQVLGIGS GSTIVHAVQR IAERVKQENL
1xtzA     19      edakraaa yravdenlkf ddhkiigigs gstvvyvaer igqylhdpkf
                                                                      
TARGET             hhhhhhh hhhhhh        ssssss      hhhhhh hhhhhhh   
1xtzA              hhhhhhh hhhhhh        ssssss    hhhhhhhh hhhhh     


TARGET    47    -----DLICI PTSFQARQLI LQYGLTLSDL DQHPEIDLAI DGADEVDAEL
1xtzA     67    yevaskfici ptgfqsrnli ldnklqlgsi eqypridiaf dgadevdenl
                                                                      
TARGET                 sss    hhhhhhh hhh               sss s   sss   
1xtzA           hhhhh  sss    hhhhhhh hhh               sss s   sss   


TARGET    92    NLIKGGGGCL TQEKIVAGYA SRFIVIADFR KDS-KNLGDR WHKGIPIEVI
1xtzA     117   qlikgggacl fqeklvstsa ktfivvadsr kkspkhlgkn wrqgvpieiv
                                                                      
TARGET          ssss     h hhhhhhhh    ssssssss                 ssssss
1xtzA           ssss     h hhhhhhhh    ssssssss                 ssssss


TARGET    141   PMAYVPVSRA VAQKFGG-EV ELRMAVN-KA GPVVTDNGNF ILDWKFDRVH
1xtzA     167   pssyvrvknd lleqlhaekv dirqggsaka gpvvtdnnnf iidadfgeis
                                                                      
TARGET             hhhhhhh hhh     ss sssss      sss      s sssss     
1xtzA               hhhhhh hhhh    ss sssss      sss      s sssss     


TARGET    189   KWSEVNTAIK MTPGVVDTGL FINMAERVYF GMQDGSVNVR EK -----  
1xtzA     217   dprklhreik llvgvvetgl fidnaskayf gnsdgsvevt ekhhhhhh  
                                                                      
TARGET           hhhhhhhhh    sssssss s     ssss ss   sssss           
1xtzA            hhhhhhhhh    sssssss s     ssss ss   sssss s   sss   



Quality


Template's ligands section
Template without ligands.
No ligands were included in the model.


Quaternary Structure Annotation of the Template
1xtz is annotated as 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: 1xtz.pdb1.gz

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 (=TETRAMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.156 (>0.5 indicates similarity)


Template Selection
 - Start SMR-Pipeline for:ee2ef4a908b5743ef208e8aa801700d5 on BC2-cluster at Fri Apr 11 05:31:14
2014 


 - 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: 
 - No template with A found
 - No template with B found
 - 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 1xtzA (72-301) 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:ee2ef4a908b5743ef208e8aa801700d5 on BC2-cluster at Fri Apr 11 05:33:46
2014 




Template Description
Match Chain SeqId

4nml: 2.60 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF PUTATIVE RIBPHOSPHATE ISOMERASE FROM TOXOPLASMA GONDII ME49 IN COMPLEMALIC ACID
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

68-301 4nmlA 34%
[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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