SWISS-MODEL Repository - Model Details

Model Overview
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1
433

Sequence
UniProt Q12463
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q12463: 4932.YOL124C

Domain
Link to: [ InterPro ]
UPF0020

Model 3D Structure
Model information:
Modelled residue range: 207 to 292
Based on template: [ 4qdk ]  
Sequence Identity [%]: 23%
Model date: 2015-05-09
Revision date: 2015-05-05

Quaternary structure information: [details]
Template (4qdk): DIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ALA: 1, GOL: 1.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

                                                       
4qdkB     8     dktivrdyfn stgfdrwrri ygdgqvnfvq kdirvghqqt vdsvvawlva
                                                                      
                                                       
4qdkB            hhhhhh    hhhhhhhhhh h      hhh hhhhhhhhhh hhhhhhhhhh


TARGET    1         VKPGTI MYDPFAGTGS FLVAGGHFGS LVIGSDIDGR MIRGKGAQVN
4qdkB     58    dg--nlpgll vcdagcgvgs lsiplaqaga lvygsdisek mvge------
                                                                      
TARGET                  ss sssss    h hhhhhhhh   ssssss  hh hh        
4qdkB                   ss sssss    h hhhhhhhh   ssssss  hh hhhh      


TARGET    47    ISANFKKYGE SSQFLDVLTM DFTNNALRNN LVIDTILCDP  ---------
4qdkB     100   aqqkaqevla ygnqptfmtq dl---aq-lg gkydtvicld vlihypteea
                                                                      
TARGET           hhhhhhhh       sssss                sss              
4qdkB           hhhhhhhhh       sssss               sssss    hh   hhhh


TARGET          ---------- ---------- ---------- ---------- ----------
4qdkB     146   samishlasl adrrlilsfa pktlgltvlk kigglfpgtr ayqhkeadir
                                                                      
TARGET                                                                
4qdkB           hhhhhhhhh    sssssss     hhhhhhh hhhh            hhhhh


TARGET          ---------- ---------- ---------- -                    
4qdkB     200   kilgdngfsi artgmtstrf yysrileavr s                    
                                                                      
TARGET                                                                
4qdkB           hhhhhhssss ssssssss   ssssssssss s                    



Quality


Template's ligands section
Ligands in the template: ALA: 1, GOL: 1.
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
4qdk 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: 4qdk.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 (=DIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.264 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 4qdkA


Template Selection
 - Start SMR-Pipeline for:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Sat May  9 06:50:00
2015 


 - 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 D found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with H found
 - No template with D found
 - No template with E found
 - No template with G found
 - No template with C found
 - No template with F found
 - No template with A found
 - 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 4qdkB (207-292) was successful 
 - ***************************************************************************
 - building model based on 3tljB (1-405) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tljA (1-405) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tm4B (1-405) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tm4A (1-405) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tm5A (1-404) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tm5B (1-404) was not successful go to next best template
 -                                      *******************************
 - building model based on 3hm2G (202-367) was successful 
 -                                     **************************************
 - building model based on 4rvgA (196-400) 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:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Sat May  9 06:54:33
2015 




Template Description
Match Chain SeqId

4qdk: CRYSTAL STRUCTURE OF MAGNESIUM PROTOPORPHYRIN IX METHYLTRA(CHLM) FROM SYNECHOCYSTIS PCC 6803 WITH BOUND SAH
Solved by: X-RAY, Resolution: 1.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

206-292 4qdkA 22%
[Model]
207-292 4qdkB 23%
[Model]

4qdj: CRYSTAL STRUCTURE OF MAGNESIUM PROTOPORPHYRIN IX METHYLTRA(CHLM) FROM SYNECHOCYSTIS PCC 6803 WITH BOUND SAM
Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

206-290 4qdjA 22%
[Model]

3tm5: CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMSINEFUNGIN
Solved by: X-RAY, Resolution: 2.27A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-404 3tm5B 13%
[Model]
1-404 3tm5A 13%
[Model]

3tlj: CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMADENOSYL-L-HOMOCYSTEINE
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-405 3tljB 13%
[Model]
1-405 3tljA 13%
[Model]

3tm4: CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMADENOSYLMETHIONINE
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-405 3tm4B 13%
[Model]
1-405 3tm4A 13%
[Model]

4rvg: CRYSTAL STRUCTURE OF MTMC IN COMPLEX WITH SAM AND TDP
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

196-400 4rvgA 11%
[Model]

4rv9: CRYSTAL STRUCTURE OF MTMC IN COMPLEX WITH SAH
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

197-367 4rv9A 10%
[Model]

3hm2: CRYSTAL STRUCTURE OF PUTATIVE PRECORRIN-6Y C5,15- METHYLTRANSFERASE TARGETED DOMAIN FROM CORYNEBACTERIUM DIPHTHERIAE
Solved by: X-RAY, Resolution: 2.21A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

195-387 3hm2D 10%
[Model]
195-368 3hm2A 12%
[Model]
200-367 3hm2B 12%
[Model]
196-367 3hm2C 11%
[Model]
201-367 3hm2H 11%
[Model]
200-367 3hm2E 11%
[Model]
196-367 3hm2F 10%
[Model]
202-367 3hm2G 12%
[Model]

4rvh: CRYSTAL STRUCTURE OF MTMC IN COMPLEX WITH SAH AND TDP-4-KE
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

196-400 4rvhA 10%
[Model]

4rvf: CRYSTAL STRUCTURE OF MTMC IN COMPLEX WITH TDP
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

196-400 4rvfA 10%
[Model]

3e05: CRYSTAL STRUCTURE OF PRECORRIN-6Y C5,15-METHYLTRANSFERASE FROM GEOBACTER METALLIREDUCENS GS-15
Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

194-380 3e05D 10%
[Model]
194-381 3e05G 10%
[Model]
194-381 3e05E 10%
[Model]
195-368 3e05A 10%
[Model]
195-380 3e05H 10%
[Model]
187-381 3e05B 10%
[Model]
185-367 3e05C 10%
[Model]
195-368 3e05F 10%
[Model]

4rvd: CRYSTAL STRUCTURE OF MTMC IN COMPLEX WITH SAM
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

196-400 4rvdA 10%
[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.




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