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Model Overview

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175

Sequence

UniProt

Q03323

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

Q03323: 4932.YDR469W

Domain

Link to: [ InterPro ]

Model 3D Structure

	Model information:
	Modelled residue range:	118 to 165
	Based on template:	[ 3g36 ]
	Sequence Identity [%]:	33%
	Model date:	2012-10-31
	Revision date:	2012-10-15

Quaternary structure information:	[details]
Template (3g36): DIMER 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 2012-10-15. 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          GGSQT RKYLNTNVTP HLLAGMRLIA VQQPEDPLRV LGEYLIEQSN
3g36D     46    vdl--qslpt rayldqtvvp illqgxavla kerppnpief lasyllknka
                                                                      
TARGET                   h hhhhhh   h hhhhhhhhhh hh    hhhh hhhhhhh   
3g36D                    h hhhhhhhhhh hhhhhhhhhh hh    hhhh hhhhhhh   


TARGET    46    ILK                                                   
3g36D     94    qfe-                                                  
                                                                      
TARGET                                                                
3g36D

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

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

Oligomer Modelling Log

Quaternary Structure Annotation of the Template 
 3g36 is annotated as DIMER 
 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: 3g36.pdb2.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 (=DIMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.246 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 3g36B

Template Selection

 - Start SMR-Pipeline for:47d76da08c5edf6c9513b0cf84dcf069 on BC2-cluster at Wed Oct 31 22:10:00
2012 


 - 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
 - Need for modeling since selected templates are the not the same as in previous update

 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                       **********************
 - building model based on 3g36D (118-165) 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:47d76da08c5edf6c9513b0cf84dcf069 on BC2-cluster at Wed Oct 31 22:10:59
2012

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

3g36: CRYSTAL STRUCTURE OF THE HUMAN DPY-30-LIKE C-TERMINAL DOMA
Solved by: X-RAY, Resolution: 1.20A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

118-165	3g36C	33%	>target ---GGSQTRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNILK >3g36C VDLQSLPTRAYLDQTVVPILLQGMAVLAKERPPNPIEFLASYLLKNKAQFE [Model]
118-165	3g36A	33%	>target ---GGSQTRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNILK- >3g36A VDLQSLPTRAYLDQTVVPILLQGMAVLAKERPPNPIEFLASYLLKNKAQFED [Model]
118-165	3g36B	33%	>target ---GGSQTRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNILK >3g36B VDLQSLPTRAYLDQTVVPILLQGMAVLAKERPPNPIEFLASYLLKNKAQFE [Model]
118-165	3g36D	33%	>target ---GGSQTRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNILK >3g36D VDLQSLPTRAYLDQTVVPILLQGMAVLAKERPPNPIEFLASYLLKNKAQFE [Model]

Downloads

download model.tgz

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.