SWISS-MODEL Repository 
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
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 KRWSPPRG IHFTVEEGDL GFTLRGNTPV QVHFLDPHCS
1vae_1#5 1 gssgssgsas --krwspprg ihftveegdl gftlrgntpv qvhfldphcs
TARGET ss s sss s sssss
1vae_1#5 ss s sss s sssss
TARGET 39 ASLAGAKEGD YIVSIQGVDC KWLTVSEVMK LLKSFGGEEV EMKVVSLLDS
1vae_1#5 49 aslagakegd yivsiqgvdc kwltvsevmk llksfggeev emkvvsllds
TARGET hhhh s ssssss sss hhhhh hhh sssss
1vae_1#5 hhhh s ssssss sss hhhhh hhh sssss
TARGET 89 TSSMHNKCAT YS
1vae_1#5 99 tssmhnksgp ssg
TARGET
1vae_1#5
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1vae is annotated as MONOMER
The template structure (1vae) 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:9d4837a2f8c26bc0dffc280836e7cb57 on BC2-cluster at Fri Feb 22 17:08:57
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
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- No template with B found
- No template with C found
- No template with D found
- No template with B found
- No template with B found
- No template with B 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:2): model based on new templates
- Send 2 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ************
- building model based on 1vaeA (509-608) was successful
- *****************************
- building model based on 3rauB (110-357) 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:9d4837a2f8c26bc0dffc280836e7cb57 on BC2-cluster at Fri Feb 22 17:11:00
2013
Template Search
| Template Description |
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1vae: SOLUTION STRUCTURE OF THE PDZ DOMAIN OF MOUSE RHOPHILIN-2 Solved by: NMR, Identified by BLAST |
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2vsv: CRYSTAL STRUCTURE OF THE PDZ DOMAIN OF HUMAN RHOPHILIN-2 Solved by: X-RAY, Resolution: 1.82A, Identified by BLAST |
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2lob: PDZ DOMAIN OF CAL (CYSTIC FIBROSIS TRANSMEMBRANE REGULATORLIGAND) Solved by: NMR, Identified by HHSEARCH |
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4e34: CRYSTAL STRUCTURE OF CFTR ASSOCIATED LIGAND (CAL) PDZ DOMAICAL36 (ANSRWPTSII) PEPTIDE Solved by: X-RAY, Resolution: 1.40A, Identified by HHSEARCH |
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4e35: CRYSTAL STRUCTURE OF CFTR ASSOCIATED LIGAND (CAL) PDZ DOMAICAL36-L (ANSRWPTSIL) PEPTIDE Solved by: X-RAY, Resolution: 1.40A, Identified by HHSEARCH |
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2dc2: SOLUTION STRUCTURE OF PDZ DOMAIN Solved by: NMR, Identified by HHSEARCH |
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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.