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 SHAGWFKDES NNEGDVVYAK
3p0lA 64 smtlysdqel aylqqgeeam qkalgils-- nqegwkkesq qdngdkvmsk
TARGET sssss s ssssss
3p0lA hhhh hhhhhhhhhh hhhhhhh sss sssss
TARGET 21 DT-PHGRMVT ISTELPMPVE DVMKETWNGM EALPEWNQNI NFAARIAAPT
3p0lA 112 vvpdvgkvfr levvvdqpme rlyeelverm eamgewnpnv k-eikvlqki
TARGET sss sssssss h hhhhhh h ss s ssssss
3p0lA ss sssss sssssss h hhhhhh h ss s ssssssss
TARGET 70 SNFDIVTYGN NDVLVVSGRE FVSARIWRKV GDGFILASRS VTVPSFKSKH
3p0lA 161 gkdtfithel aaenlvgprd fvsvrcakrr gstcvlagma tdfgnm-peq
TARGET sssssss ss sss ssssssssss ssssssss s
3p0lA ssssssss ss sss ssssssssss ssssssss s
TARGET 120 KGKVRAHLHL AGARFRPNPE NPETTLTDVV MLADLKGYLP KMIVNQVIGR
3p0lA 213 kgviraehgp tcmvlhplag spsktkltwl lsidlkgwlp ksiinqvlsq
TARGET ssssss ssssssss ssssssss ssss hhhhhhhhh
3p0lA ssssss ssssssss ssssssss ssss hhhhhhhhh
TARGET 170 IMI ------ ----
3p0lA 263 tqvdfanhlr krle
TARGET hhh
3p0lA hhhhhhhhhh hh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3p0l 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: 3p0l.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 0.338 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:c8fa20c3c1339547c58313a8a8714b21 on BC2-cluster at Wed Feb 20 22:50:51
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:
- 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 1em2A (73-254) was not successful go to next best template
- ********************************************************
- building model based on 3p0lC (58-239) was not successful go to next best template
- *****************************************************
- building model based on 3p0lA (68-239) 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:c8fa20c3c1339547c58313a8a8714b21 on BC2-cluster at Wed Feb 20 22:52:21
2013
Template Search
| Template Description |
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2ns9: CRYSTAL STRUCTURE OF PROTEIN APE2225 FROM AEROPYRUM PERNIXK1, PFAM COXG Solved by: X-RAY, Resolution: 1.80A, 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.