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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: 2013-11-24
Revision date: 2013-11-19

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 2013-11-19. 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 0.19 (>0.5 indicates similarity)


Template Selection
 - Start SMR-Pipeline for:ee2ef4a908b5743ef208e8aa801700d5 on BC2-cluster at Sun Nov 24 13:11:30
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: 
 - No template with A found
 - No template with A found
 - No template with B 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 Sun Nov 24 13:22:12
2013 




Template Description
Match Chain SeqId

1xtz: CRYSTAL STRUCTURE OF THE S. CEREVISIAE D-RIBOSE-5-PHOSPHATISOMERASE: COMPARISON WITH THE ARCHEAL AND BACTERIAL ENZYMES
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

72-302 1xtzA 46%
[Model]

3ixq: STRUCTURE OF RIBOSE 5-PHOSPHATE ISOMERASE A FROM METHANOCALDOCOCCUS JANNASCHII
Solved by: X-RAY, Resolution: 1.78A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-301 3ixqD 42%
[Model]
70-301 3ixqC 42%
[Model]
70-301 3ixqB 42%
[Model]
70-301 3ixqA 42%
[Model]

1lk5: STRUCTURE OF THE D-RIBOSE-5-PHOSPHATE ISOMERASE FROM PYROCOCCUS HORIKOSHII
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

68-301 1lk5A 40%
[Model]
68-301 1lk5D 40%
[Model]
68-301 1lk5C 40%
[Model]
68-301 1lk5B 40%
[Model]

1lk7: STRUCTURE OF D-RIBOSE-5-PHOSPHATE ISOMERASE FROM IN COMPLEWITH PHOSPHO-ERYTHRONIC ACID
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

68-301 1lk7B 40%
[Model]
68-301 1lk7A 40%
[Model]
68-301 1lk7D 40%
[Model]
68-301 1lk7C 40%
[Model]

1uj4: CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS RIBOSE-5- PHOSPHATE ISOMERASE
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-298 1uj4A 39%
[Model]

1uj6: CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS RIBOSE-5- PHOSPHATE ISOMERASE COMPLEXED WITH ARABINOSE-5-PHOSPHATE
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-298 1uj6A 39%
[Model]

1uj5: CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS RIBOSE-5- PHOSPHATE ISOMERASE COMPLEXED WITH RIBOSE-5-PHOSPHATE
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-298 1uj5A 39%
[Model]

3hhe: CRYSTAL STRUCTURE OF RIBOSE-5-PHOSPHATE ISOMERASE A FROM BARTONELLA HENSELAE
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-301 3hheB 38%
[Model]
70-301 3hheA 38%
[Model]

1o8b: STRUCTURE OF ESCHERICHIA COLI RIBOSE-5-PHOSPHATE ISOMERASERPIA, COMPLEXED WITH ARABINOSE-5-PHOSPHATE.
Solved by: X-RAY, Resolution: 1.25A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

119-298 1o8bA 35%
[Model]
70-298 1o8bB 33%
[Model]

2f8m: RIBOSE 5-PHOSPHATE ISOMERASE FROM PLASMODIUM FALCIPARUM
Solved by: X-RAY, Resolution: 2.09A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

69-301 2f8mA 35%
[Model]
71-303 2f8mB 35%
[Model]

1m0s: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG ID IR21)
Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

68-300 1m0sB 34%
[Model]
68-300 1m0sA 34%
[Model]

1ks2: CRYSTAL STRUCTURE ANALYSIS OF THE RPIA, STRUCTURAL GENOMICPROTEIN EC1268.
Solved by: X-RAY, Resolution: 1.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-299 1ks2A 33%
[Model]
70-299 1ks2B 33%
[Model]

1lkz: CRYSTAL STRUCTURE OF D-RIBOSE-5-PHOSPHATE ISOMERASE (RPIA)FROM ESCHERICHIA COLI.
Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

68-299 1lkzB 33%
[Model]
68-299 1lkzA 33%
[Model]

3uw1: CRYSTAL STRUCTURE OF RIBOSE-5-PHOSPHATE ISOMERASE A FROM BTHAILANDENSIS WITH RIBOSE-5-PHOSPHATE
Solved by: X-RAY, Resolution: 1.71A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

68-302 3uw1A 33%
[Model]

4io1: CRYSTAL STRUCTURE OF RIBOSE-5-ISOMERASE A FROM FRANCISELLA
Solved by: X-RAY, Resolution: 1.65A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

69-299 4io1A 32%
[Model]
72-299 4io1B 33%
[Model]

3u7j: CRYSTAL STRUCTURE OF RIBOSE-5-PHOSPHATE ISOMERASE A FROM BTHAILANDENSIS
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

68-302 3u7jA 33%
[Model]

4gmk: CRYSTAL STRUCTURE OF RIBOSE 5-PHOSPHATE ISOMERASE FROM THEBACTERIUM LACTOBACILLUS SALIVARIUS UCC118
Solved by: X-RAY, Resolution: 1.72A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-301 4gmkA 33%
[Model]
72-301 4gmkB 33%
[Model]

3enq: SUBSTRATE AND INHIBITOR COMPLEXES OF RIBOSE 5-PHOSPHATE ISOMERASE A FROM VIBRIO VULNIFICUS YJ016
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-300 3enqB 32%
[Model]
70-300 3enqA 32%
[Model]

4m8l: CRYSTAL STRUCTURE OF RPIA-R5P COMPLEX
Solved by: X-RAY, Resolution: 2.37A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-299 4m8lC 32%
[Model]
68-299 4m8lA 32%
[Model]
69-299 4m8lD 32%
[Model]
70-299 4m8lB 32%
[Model]

3l7o: CRYSTAL STRUCTURE OF RIBOSE-5-PHOSPHATE ISOMERASE A FROM SMUTANS UA159
Solved by: X-RAY, Resolution: 1.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

72-301 3l7oB 33%
[Model]
72-302 3l7oA 32%
[Model]

3kwm: CRYSTAL STRUCTURE OF RIBOSE-5-ISOMERASE A
Solved by: X-RAY, Resolution: 2.37A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

69-299 3kwmD 32%
[Model]
69-299 3kwmA 32%
[Model]
69-299 3kwmC 32%
[Model]
70-299 3kwmB 32%
[Model]

3enw: SUBSTRATE AND INHIBITOR COMPLEXES OF RIBOSE 5-PHOSPHATE ISOMERASE FROM VIBRIO VULNIFICUS YJ016
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-300 3enwB 32%
[Model]
70-300 3enwA 32%
[Model]

3env: SUBSTRATE AND INHIBITOR COMPLEXES OF RIBOSE 5-PHOSPHATE ISOMERASE FROM VIBRIO VULNIFICUS YJ016
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

70-300 3envB 32%
[Model]
70-300 3envA 32%
[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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