SWISS-MODEL Repository - Model Details

Model Overview
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1
192

Sequence
UniProt P07321 Erythropoietin
Mus musculus (Mouse).
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
P07321: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
EPO_TPO

Model 3D Structure
Model information:
Modelled residue range: 27 to 192
Based on template: [ 1buy ]  
Sequence Identity [%]: 78%
Model date: 2013-11-24
Revision date: 2013-11-19

Quaternary structure information: [details]
Template (1buy): MONOMER
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       APPRLICD SRVLERYILE AKEAENVTMG CAEGPRLSEN ITVPDTKVNF
1buyA     1       apprlicd srvlerylle akeaekittg caehcslnek itvpdtkvnf
                                                                      
TARGET                      hhhhhhhhh hhhhhhhh              sss      h
1buyA                       hhhhhhhhh hhhhhhhh              sss      h


TARGET    49    YAWKRMEVEE QAIEVWQGLS LLSEAILQAQ ALLANSSQPP ETLQLHIDKA
1buyA     49    yawkrmevgq qavevwqgla llseavlrgq allvkssqpw eplqlhvdka
                                                                      
TARGET          hhh    hhh hhhhhhhhhh hhhhhhhhhh hhhhh         hhhhhhh
1buyA                  hhh hhhhhhhhhh hhhhhhhhhh hhhhh         hh   hh


TARGET    99    ISGLRSLTSL LRVLGAQKEL MSPPDTTPPA PLRTLTVDTF CKLFRVYANF
1buyA     99    vsglrslttl lralgaqkea isppdaasaa plrtitadtf rklfrvysnf
                                                                      
TARGET          hhhhhhhhhh hhh                       sss    hhhhh   hh
1buyA           hhhhhhhhhh hhh                       sss    hhhhhhhhhh


TARGET    149   LRGKLKLYTG EVCRRGDR                                   
1buyA     149   lrgklklytg eacrtgdr-                                  
                                                                      
TARGET          hhhhhhhhhh hhh                                        
1buyA           h   hhhhhh hhh                                        



Quality


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


Quaternary Structure Annotation of the Template
1buy is annotated as MONOMER
The template structure (1buy) was solved by NMR and does not contain any quaternary structure annotation
The template is annotated by the number of chains found in the PDB file

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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.102 (>0.5 indicates similarity)


Template Selection
 - Start SMR-Pipeline for:76810fde2f1ede7e8151cde3177a0c92 on BC2-cluster at Sun Nov 24 12:20:12
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

 - No A3m found

 - No template with B found
 - No template with C found
 - 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 1buyA (27-192) 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:76810fde2f1ede7e8151cde3177a0c92 on BC2-cluster at Sun Nov 24 12:21:00
2013 




Template Description
Match Chain SeqId

1buy: HUMAN ERYTHROPOIETIN, NMR MINIMIZED AVERAGE STRUCTURE
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

27-192 1buyA 78%
[Model]

1eer: CRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITSRECEPTOR AT 1.9 ANGSTROMS
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

27-192 1eerA 77%
[Model]

1cn4: ERYTHROPOIETIN COMPLEXED WITH EXTRACELLULAR DOMAINS OF ERYTHROPOIETIN RECEPTOR
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

28-188 1cn4C 76%
[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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