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 QFKSIQ HHLRTAQEHD KRDPVVAYYC RLYAMQTGMK
2lxlA 1 maalaplppl pa--qfksiq hhlrtaqehd krdpvvayyc rlyamqtgmk
TARGET h hhhhhhhhhh h hhhhhh hhhhhhhhhh
2lxlA h hhhhhhhhhh h hhhhhh hhhhhhhhhh
TARGET 37 IDSKTPECRK FLSKLMDQLE ALKKQLGDNE AVTQEIVGCA HLENYALKMF
2lxlA 49 idsktpecrk flsklmdqle alkkqlgdne aitqeivgca hlenyalkmf
TARGET h hhhhh hhhhhhhhhh hhhhhh h hh hhhhh hhhhhhhhhh
2lxlA h hhhhh hhhhhhhhhh hhhhhh h hh hhhhh hhhhhhhhhh
TARGET 87 LYADNEDRAG RFHKNMIKSF YTASLLIDVI TVFGELTDEN VKHRKYARWK
2lxlA 99 lyadnedrag rfhknmiksf ytasllidvi tvfgeltden vkhrkyarwk
TARGET hhhhhhhh hhhhhh hhhhhhhhhh hh hhh hhhhhhhhhh
2lxlA hhhhhhhh hhhhhh hhhhhhhhhh hh hhh hhhhhhhhhh
TARGET 137 ATYIHNCLKN GETPQ
2lxlA 149 atyihnclkn getpq-
TARGET hhhhhhhhhh
2lxlA hhhhhhhhhh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2lxl 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: 2lxl.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 0.22 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:c588e3c4bd35c78e089846c81b3adebb on BC2-cluster at Sat Feb 23 04:15:39
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:
- Skip Template HHsearch issue
- Skip Template HHsearch issue
- 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:1): model based on new templates
- Send 1 Templates for modeling
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- ***************************************
- building model based on 2lxlA (13-163) 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:c588e3c4bd35c78e089846c81b3adebb on BC2-cluster at Sat Feb 23 04:17:04
2013
Template Search
| Template Description |
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2lxl: LIP5(MIT)2 Solved by: NMR, Identified by BLAST |
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2lxm: LIP5-CHMP5 Solved by: NMR, Identified by BLAST |
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2luh: NMR STRUCTURE OF THE VTA1-VPS60 COMPLEX Solved by: NMR, Identified by HHSEARCH |
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2rkk: CRYSTAL STRUCTURE OF S.CEREVISIAE VTA1 N-TERMINAL DOMAIN Solved by: X-RAY, Resolution: 2.90A, 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.