SWISS-MODEL Repository - Model Details

Model Overview
Click on the bars to get more details about individual Models or experimental structures
1
597

Sequence
UniProt Q11181 Uncharacterized protein C05D10.4
Caenorhabditis elegans.
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
Q11181: 6239.C05D10.4b

Domain
Link to: [ InterPro ]
SAM_2

Model 3D Structure
Model information:
Modelled residue range: 397 to 465
Based on template: [ 2gle ]  
Sequence Identity [%]: 26%
Model date: 2013-11-23
Revision date: 2013-11-19

Quaternary structure information: [details]
Template (2gle): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: none.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-11-19. 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 ]



Alignment

TARGET    1        KTVKEWS LDDVLLWLQS AQMDDVAGLL IGYDLRGEDL LQWNDQTLAQ
2gleA     1     g--hmvhews vqqvshwlvg lsldqyvsef saqnisgeql lqldgnklka
                                                                      
TARGET                       hhhhhhh      hhhhhh hh    hhhh     hhhhhh
2gleA                        hhhhhhh      hhhhhh hhh   hhhh    hhhhhhh


TARGET    48    LGVSNPEIRK KLLDDLSKII EN ---                          
2gleA     49    lgmtssqdra lvkkklkemk msleka                          
                                                                      
TARGET               hhhhh hhhhhh   h hh                              
2gleA                hhhhh hhhhhh   h hhhhh                           



Quality


Template's ligands section
Template without ligands.
No ligands were included in the model.


Quaternary Structure Annotation of the Template
2gle is annotated as MONOMER
The template structure (2gle) was solved by NMR and does not contain any quaternary structure annotation
The template is annotated by the number of chains found in the PDB file

Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 26.087) 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:9cbe302d371d61b5bd50e49e6b5c7412 on BC2-cluster at Sat Nov 23 18:11:30
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 modified template library 
 - Summarize templates: 
 - No template with C found
 - No template with D found
 - 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 2gleA (397-465) 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:9cbe302d371d61b5bd50e49e6b5c7412 on BC2-cluster at Sat Nov 23 18:24:17
2013 




Template Description
Match Chain SeqId

2gle: SOLUTION STRUCTURE OF NEURABIN SAM DOMAIN
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

397-465 2gleA 26%
[Model]

3bs7: CRYSTAL STRUCTURE OF THE STERILE ALPHA MOTIF (SAM) DOMAIN OF HYPHEN/AVEUGLE
Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

397-465 3bs7A 25%
[Model]
397-465 3bs7B 25%
[Model]

2l5y: NMR STRUCTURE OF CALCIUM-LOADED STIM2 EF-SAM.
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

391-460 2l5yA 25%
[Model]

2k60: NMR STRUCTURE OF CALCIUM-LOADED STIM1 EF-SAM
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

391-461 2k60A 23%
[Model]

2f3n: CRYSTAL STRUCTURE OF THE NATIVE SHANK SAM DOMAIN.
Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

399-462 2f3nA 22%
[Model]
399-462 2f3nB 22%
[Model]
399-459 2f3nC 23%
[Model]

3bq7: SAM DOMAIN OF DIACYLGLYCEROL KINASE DELTA1 (E35G)
Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

398-464 3bq7B 24%
[Model]
397-464 3bq7A 24%
[Model]
398-464 3bq7F 24%
[Model]
397-465 3bq7C 23%
[Model]
398-465 3bq7D 24%
[Model]
397-464 3bq7E 24%
[Model]

2f44: CRYSTAL STRUCTURE OF THE ZINC-BOUND SHANK SAM DOMAIN
Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

399-462 2f44A 22%
[Model]
399-462 2f44B 22%
[Model]
399-459 2f44C 23%
[Model]

2ean: SOLUTION STRUCTURE OF THE N-TERMINAL SAM-DOMAIN OF HUMAN KIAA0902 PROTEIN (CONNECTOR ENHANCER OF KINASE SUPPRESSOROF RAS 2)
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

396-470 2eanA 21%
[Model]

3bs5: CRYSTAL STRUCTURE OF HCNK2-SAM/DHYP-SAM COMPLEX
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

397-465 3bs5A 25%
[Model]
397-465 3bs5B 21%
[Model]

2e8o: SOLUTION STRUCTURE OF THE N-TERMINAL SAM-DOMAIN OF THE SAMDOMAIN AND HD DOMAIN CONTAINING PROTEIN 1 (DENDRITIC CELLDERIVED IFNG-INDUCED PROTEIN) (DCIP) (MONOCYTE PROTEIN 5)(MOP-5)
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

399-469 2e8oA 21%
[Model]

1wwv: SOLUTION STRUCTURE OF THE SAM DOMAIN OF HUMAN CONNECTOR ENHANCER OF KSR-LIKE PROTEIN CNK1
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

395-466 1wwvA 21%
[Model]

3tad: CRYSTAL STRUCTURE OF THE LIPRIN-ALPHA/LIPRIN-BETA COMPLEX
Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

383-466 3tadA 20%
[Model]
382-465 3tadB 20%
[Model]

1v85: STERILE ALPHA MOTIF (SAM) DOMAIN OF MOUSE BIFUNCTIONAL APOPTOSIS REGULATOR
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

393-463 1v85A 19%
[Model]

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.




SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.