SWISS-MODEL Repository 
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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 EQPAGG- EGFHLHGVQE NSPAQQAGLE PYFDFIITIG HSRLNKENDT
3rleA 7 v--eipgggt egyhvlrvqe nspghragle pffdfivsin gsrlnkdndt
TARGET sssssssss hhhhh ssssssss sss h
3rleA s sssssssss hhhhh ssssssss sss h
TARGET 47 LKALLKANVE KPVKLEVFNM KTMKVREVEV VPSNMWGGQG LLGASVRFCS
3rleA 55 lkdllkanve kpvkxliyss ktlelretsv tpsnlwggqg llgvsirfcs
TARGET hhhhhhh ssssssss sssssss ssssssss
3rleA hhhhhhh ssssssss sssssss ssssssss
TARGET 97 FRRASEHVWH VLDVEPSSPA ALAGLCPYTD YIVGSDQILQ ESEDFFTLIE
3rleA 105 fdganenvwh vlevesnspa alaglrphsd yiigadtvxn esedlfslie
TARGET ss sssss hh hhh ss sss hhhhhh
3rleA s ss sssss hh hhh ss sss hhhhhh
TARGET 147 SHEGKPLKLM VYNSESDSCR EVTVTPNAAW GGEGSLGCGI GYGYLHRIPT
3rleA 155 theakplkly vyntdtdncr eviitpnsaw ggegslgcgi gygylhript
TARGET h ssss ssss sss ssss ssss s
3rleA h ssss ssss sss ssss ssss s
TARGET 197 QP -
3rleA 205 rpfe
TARGET
3rleA
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3rle is annotated as MONOMER
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: 3rle.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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.272 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:a15b7b5a0e9fa18947788aba7bdb5847 on BC2-cluster at Fri Feb 22 17:54:09
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 C found
- No template with D found
- No template with C found
- No template with D 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 3rleA (8-205) 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:a15b7b5a0e9fa18947788aba7bdb5847 on BC2-cluster at Fri Feb 22 17:55:17
2013
Template Search
| Template Description |
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4edj: CRYSTAL STRUCTURE OF THE GRASP55 GRASP DOMAIN WITH A PHOSPMUTATION (S189D) Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST |
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3rle: CRYSTAL STRUCTURE OF GRASP55 GRASP DOMAIN (RESIDUES 7-208) Solved by: X-RAY, Resolution: 1.65A, Identified by BLAST |
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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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2lob: PDZ DOMAIN OF CAL (CYSTIC FIBROSIS TRANSMEMBRANE REGULATORLIGAND) Solved by: NMR, 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.