SWISS-MODEL Repository - Model Details

Model Overview
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1
433

Sequence
UniProt Q12463 tRNA (guanine(10)-N2)-methyltransferase (tRNA [Gm10] methyltransferase)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
Q12463: 4932.YOL124C

Domain
Link to: [ InterPro ]
UPF0020

Model 3D Structure
Model information:
Modelled residue range: 189 to 291
Based on template: [ 4o29 ]  
Sequence Identity [%]: 13%
Model date: 2014-04-10
Revision date: 2014-04-08

Quaternary structure information: [details]
Template (4o29): MONOMER
Model built: SINGLE CHAIN

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

Alignment

                                                       
4o29A     65535  almakrlvee lerdgivkse rvkralltvp reefvlpeyr mmayedrplp
                                                                      
                                                       
4o29A            hhhhhhhhh hhhh     h hhhhhhhh           hh         ss


TARGET    1          GTTSF EAELSLVSAN IAQVKPGTIM YDPFAGTGSF L---VAGGHF
4o29A     49    lfa--gatis aphmvammce lieprpgmki levgtgsgyh aavcaeaiek
                                                                      
TARGET                      hhhhhhhhh h      sss ssss                 
4o29A           s     sss   hhhhhhhhh h      sss ssss    hh hhhhhhhh  


TARGET    43    GSLVIGSDID GRMIRGKGAQ VNISANFKKY GESSQFLDVL TMDFTNNALR
4o29A     97    kgriytieiv kelavf---- --aaqnlerl gywgv-vevy hgdgkkg-le
                                                                      
TARGET            ssssss   hhhh          hhhhhh         sss ss        
4o29A             ssssss   hhhhhh       hhhhhhh      s ssss ss        


TARGET    93    NNLVIDTILC D -------- ---------- ---------- ----------
4o29A     139   khapfdaiiv taaadvippa lirqlkdggv mvipveerlg qvlykvvkrg
                                                                      
TARGET                ssss s                                          
4o29A                sssss s        h hhhh    ss sssssss  s sssssssss 


TARGET          ---------- -------                                    
4o29A     189   dkiekkaity vmfvplr                                    
                                                                      
TARGET                                                                
4o29A            sssssssss s                                          



Quality


Template's ligands section
Ligands in the template: ALA: 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
4o29 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: 4o29.pdb1.gz

Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 13.208) 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:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Thu Apr 10 19:59:44
2014 


 - 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 A found
 - No template with B 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 A found
 - No template with C found
 - No template with F found
 - No template with B found
 - No template with A found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                    *******************
 - building model based on 4o29A (189-291) was successful 
 -                                   **********************************
 - building model based on 4ineA (185-368) 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 4ponA (198-406) 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 Thu Apr 10 20:04:34
2014 




Template Description
Match Chain SeqId

4o29: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE FROM PYROBACULUIN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

189-291 4o29A 13%
[Model]

4lwo: CRYSTAL STRUCTURE OF PRMT6
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

208-300 4lwoA 13%
[Model]
208-299 4lwoB 13%
[Model]
208-299 4lwoG 13%
[Model]
208-300 4lwoE 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]

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]

4lwp: CRYSTAL STRUCTURE OF PRMT6-SAH
Solved by: X-RAY, Resolution: 2.35A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

208-299 4lwpA 13%
[Model]
207-300 4lwpB 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]

4ine: CRYSTAL STRUCTURE OF N-METHYL TRANSFERASE (PMT-2) FROM CAEELEGANT COMPLEXED WITH S-ADENOSYL HOMOCYSTEINE AND PHOSPHOETHANOLAMINE
Solved by: X-RAY, Resolution: 1.45A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

185-367 4ineB 13%
[Model]
185-368 4ineA 13%
[Model]

4iv8: CRYSTAL STRUCTURE OF N-METHYL TRANSFERASE FROM PLASMODIUM COMPLEXED WITH S-ADENOSYL METHIONINE
Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

185-369 4iv8B 12%
[Model]
185-369 4iv8A 12%
[Model]

4poo: THE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS YTQB IN COMPLEX
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

196-292 4pooB 11%
[Model]
201-366 4pooA 8%
[Model]

4nec: CONVERSION OF A DISULFIDE BOND TO A THIOACETAL GROUP DURINECHINOMYCIN BIOSYNTHESIS
Solved by: X-RAY, Resolution: 1.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

205-365 4necA 11%
[Model]
203-367 4necB 10%
[Model]
201-366 4necC 10%
[Model]
200-366 4necD 11%
[Model]

4iv0: CRYSTAL STRUCTURE OF N-METHYL TRANSFERASE FROM PLASMODIUM COMPLEXED WITH S-ADENOSYL METHIONINE AND PHOSPHATE
Solved by: X-RAY, Resolution: 1.40A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

186-369 4iv0A 11%
[Model]
186-367 4iv0B 11%
[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 ]  

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

4oa8: X-RAY CRYSTAL STRUCTURE OF O-METHYLTRANSFERASE FROM ANAPLAPHAGOCYTOPHILUM IN APO FORM
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

192-362 4oa8A 8%
[Model]
191-362 4oa8B 8%
[Model]

4oa5: X-RAY CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE FROM ANAPHAGOCYTOPHILUM BOUND TO SAH SOLVED BY IODIDE SAD PHASING
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

188-362 4oa5A 8%
[Model]
188-362 4oa5C 8%
[Model]
188-362 4oa5B 8%
[Model]
192-362 4oa5E 8%
[Model]
191-362 4oa5D 8%
[Model]
191-362 4oa5F 8%
[Model]

4pon: THE CRYSTAL STRUCTURE OF A PUTATIVE SAM-DEPENDENT METHYLTRYTQB, FROM BACILLUS SUBTILIS
Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

206-363 4ponB 6%
[Model]
198-406 4ponA 6%
[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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