SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | O08852 |
Database: TrEMBL (Unreviewed)  |
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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
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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 ]
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Alignment
TARGET 1 ATLVGPHG PLASGQPADF HITSSLPISS TRWNFGDGSP EVDMASPAAT
1b4r_1#2 8 atlvgphg plasgqlaaf hiaaplpvta trwdfgdgsa evdaagpaas
TARGET sssss sssss sss ss ssssss ss ssssssssss
1b4r_1#2 sssss sssss sss ss ssssss ss ssssssssss
TARGET 49 HFYVLPGSYH MTVVLALGAG SALLETEVQV EA
1b4r_1#2 56 hryvlpgryh vtavlalgag sallgtdvqv ea-
TARGET sss ssss sssssss s ssssssssss
1b4r_1#2 sss ssss sssssss s ssssssssss
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1b4r is annotated as MONOMER
The template structure (1b4r) 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
The quaternary structure can be assumed to be identical
Model was succesfully built as MONOMER.
Template Selection
- Start SMR-Pipeline for:70d511dcc197d2022ccc0a70ae1ee0d2 on BC2-cluster at Sun Feb 17 06:15:12
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
- Warning: sequence length exceeded the limit of 1500 residues
- HHsearch profile build is skipped
FATAL - No A3m found
- Warning: Oligomer Prediction was not successfull!
- 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 Sun Feb 17 06:15:57
2013
Template Search
| Template Description |
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1b4r: PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1 Solved by: NMR, Identified by BLAST |
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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.