SWISS-MODEL Repository - Model Details

Model Overview
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1
4293

Sequence
UniProt O08852
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Lectin_C
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PKD
PLAT
WSC
GPS
REJ
PKD_channel
LRR_8

Model 3D Structure
Model information:
Modelled residue range: 275 to 354
Based on template: [ 1b4r ]  
Sequence Identity [%]: 76%
Model date: 2014-10-07
Revision date: 2014-10-06

Quaternary structure information: [details]
Template (1b4rA): Unknown
Model: 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 ]

Alignment

TARGET    1       ATLVGPHG PLASGQPADF HITSSLPISS TRWNFGDGSP EVDMASPAAT
1b4rA     8       atlvgphg plasgqlaaf hiaaplpvta trwdfgdgsa evdaagpaas
                                                                      
TARGET             sssss        sssss sss     ss ssssss  ss ssssssssss
1b4rA              sssss        sssss sss     ss ssssss  ss ssssssssss


TARGET    49    HFYVLPGSYH MTVVLALGAG SALLETEVQV EA                   
1b4rA     56    hryvlpgryh vtavlalgag sallgtdvqv ea-                  
                                                                      
TARGET          sss   ssss sssssss  s ssssssssss                      
1b4rA           sss   ssss sssssss  s ssssssssss                      



Quality


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


Oligomer Annotation of the Template structure
Sorry, we haven't found any oligomeric annotation for this template.
Either the complex was too large (>60 chains) or the structures was excluded for other reasons.
Please contact help@swissmodel.org for more information!


Template Selection
 - Start SMR-Pipeline for:70d511dcc197d2022ccc0a70ae1ee0d2 on BC2-cluster at Tue Oct  7 16:57:25
2014 


 - 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

 - Warning: sequence length exceeded the limit of 1000 residues
 - HHsearch profile build is skipped
 - No A3m found

 - A3m will not be built  -  sequence too long

 - Skipping oligomeric state prediction due to too many templates for cluster: 275_354
 - Warning: Oligomer Prediction was not successfull!

 - Warning: clustersMergedFile not 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 1b4rA (275-354) 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:70d511dcc197d2022ccc0a70ae1ee0d2 on BC2-cluster at Tue Oct  7 16:57:37
2014 




Template Description
Match Chain SeqId

1b4r: PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

275-354 1b4rA 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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