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 QNSY TELLDACSEQ VKFGVIYLHD PLLDNHMDYV
3ph9A 31 pqtlsrgwgd ditw--vqty eeglfyaqks kkplmvihhl edcqysqalk
TARGET h hhhhhhhhhh sssssss hhhhhhh
3ph9A h hhhhhhhhhh sssssss hhhhhhh
TARGET 35 NKILCSEAFV NMIRKYQVLL WYGDVTTSEG LQVSNALKIR QYPLLGIISL
3ph9A 79 kvfaqneeiq emaqn-kfim lnlmhettdk ---nlspdgq yvprimfvdp
TARGET hhhh hhh hhh ssss sss hh sssss
3ph9A hhh hhhh hhhh ss sss ssssss
TARGET 85 KAEKKIELIA RVEGSIS -- ---------- ---------- ---
3ph9A 125 slt----vra diagrysnrl ytyeprdlpl lienmkkalr liq
TARGET hhhh
3ph9A s ss hhh hhhhhhhhh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3ph9 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: 3ph9.pdb1.gz
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 11.881) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode
The target structure was calculated as SINGLE CHAIN
Template Selection
- Start SMR-Pipeline for:cd28c9764560508b926e4a9760be8b39 on BC2-cluster at Mon Feb 18 16:37:40
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- 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 3ph9A (166-266) 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:cd28c9764560508b926e4a9760be8b39 on BC2-cluster at Mon Feb 18 16:38:33
2013
Template Search
| Template Description |
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3ph9: CRYSTAL STRUCTURE OF THE HUMAN ANTERIOR GRADIENT PROTEIN 3 Solved by: X-RAY, Resolution: 1.83A, Identified by HHSEARCH |
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2lns: SOLUTION STRUCTURE OF AGR2 RESIDUES 41-175 Solved by: NMR, Identified by HHSEARCH |
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2lnt: SOLUTION STRUCTURE OF E60A MUTANT AGR2 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.