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 VLSQRQRE ELNQAIADYL GSNGYADSLE TFRK--EADL STEVEKKFGG
1uuj_1#3 2 vlsqrqrd elnraiadyl rsngyeeays vfkkeaeldx neeldkkyag
TARGET hhhhh hhhhhhhhhh h hhhhhh hh hhhhh h
1uuj_1#3 hhhhh hhhhhhhhhh hh hhhhh hhhhhh hhhhh h
TARGET 47 LLEKKWTSVI RLQKKVMELE AKLTEAEK - VLSQRQREE LNQAIADYLG
1uuj_1#3 50 llekkwtsvi rlqkkvxele sklneake-- -vlsqrqrde lnraiadylr
*
TARGET hhhhh hh hhhhhhhhhh hhhhhh hhhhhh hhhhhhhhhh
1uuj_1#3 hhhhh hh hhhhhhhhhh hhhhh hhhhhh hhhhhhhhhh
TARGET 94 SNGYADSLET FRK--EADLS TEVEKKFGGL LEKKWTSVIR LQKKVMELEA
1uuj_1#3 21 sngyeeaysv fkkeaeldxn eeldkkyagl lekkwtsvir lqkkvxeles
TARGET hhhhhhh h hhhh h hhhh hhh hhhhhhhhhh
1uuj_1#3 h hhhhhh hhhhh hhhh h hhhh hhh hhhhhhhhhh
TARGET 142 KLTEAEKE - - VLSQRQRE ELNQAIADYL GSNGYADSLE TFRK--EADL
1uuj_1#3 71 klneakee-f --vlsqrqrd elnraiadyl rsngyeeays vfkkeaeldx
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TARGET hhhhhhh hhhhh hhhhhhhhhh h hhhhhh hhh
1uuj_1#3 hhhhhhh hhhhh hhhhhhhhhh h hhhhhh hhhhhh
TARGET 186 STEVEKKFGG LLEKKWTSVI RLQKKVMELE AKLTEA - M VLSQRQREEL
1uuj_1#3 40 neeldkkyag llekkwtsvi rlqkkvxele sklnea---x vlsqrqrdel
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TARGET hhhhh h hhhhhhhhhh hhhhhhhhhh hhhhh hhhhhhh
1uuj_1#3 hhhhh hhhhhhhhhh hhhhhhhhhh hhhh hhhhhhh
TARGET 233 NQAIADYLGS NGYADSLETF RK--EADLST EVEKKFGGLL EKKWTSVIRL
1uuj_1#3 12 nraiadylrs ngyeeaysvf kkeaeldxne eldkkyagll ekkwtsvirl
TARGET hhhhhhhhh hhhhhhhh h hhhhhh h hhhhhhhhhh
1uuj_1#3 hhhhhhhhh hhhhhhhh hhhh h hhhhhh h hhhhhhhhhh
TARGET 281 QKKVMELEAK LTEAEKE
1uuj_1#3 62 qkkvxelesk lneakeef
TARGET hhhhhhhhhh hhhhhhh
1uuj_1#3 hhhhhhhhhh hhhhhhh
Template's ligands section
Ligands in the template:ACT : 1,BEZ : 1,SO4 : 4.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1uuj is annotated as TETRAMER
PISA was used to annotate the quaternary structure, because the author assignment was
The template was built based on the following PISA annotation file: 1uuj_assembly.xml.gz
Quaternary Structure Modelling of the Target Protein
The quaternary structure can be assumed to be identical
To build the complex the following chains of the complex has been additionally identified: 1uujD 1uujC 1uujA
Model was succesfully built as TETRAMER.
Template Selection
- Start SMR-Pipeline for:0df75cd34451ff7946319bc58a2e76d0 on BC2-cluster at Fri Feb 22 09:05:51
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 2 go for
modeling ...
FATAL - No A3m found
- No template with Q found
- No template with R found
- No template with M found
- No template with N found
- No template with I found
- No template with J found
- No template with E found
- No template with F found
- No template with A found
- No template with B found
- Warning: Oligomer Prediction was not successfull!
- 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 1uujB (4-75) was successful
- **************************************************************
- building model based on 1vyhT (93-409) 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:0df75cd34451ff7946319bc58a2e76d0 on BC2-cluster at Fri Feb 22 09:07:33
2013
Template Search
| Template Description |
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1uuj: N-TERMINAL DOMAIN OF LISSENCEPHALY-1 PROTEIN (LIS-1) Solved by: X-RAY, Resolution: 1.75A, Identified by BLAST |
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1vyh: PAF-AH HOLOENZYME: LIS1/ALFA2 Solved by: X-RAY, Resolution: 3.40A, Identified by BLAST |
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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.