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: 199 to 363
Based on template: [ 2igt ]  
Sequence Identity [%]: 15%
Model date: 2014-07-16
Revision date: 2014-07-15

Quaternary structure information: [details]
Template (2igt): TRIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: FMT: 3, GOL: 1, SAM: 1.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

                                                       
2igtB     65530  enlyfqgxqr tgelpaehvp vilessgagd fhlidsgngl kleqygdyrv
                                                                      
                                                       
2igtB                           sss   sssss    s sssssss ss ssssss sss


                                                       
2igtB     44    vrpeaqalwr plvpdrvwqn adaiftgdgx grwrfpkeal getwplsllg
                                                                      
                                                       
2igtB           ssss            hhhh    ssss      sss        sssssss  


TARGET    1                                 LVSA NIAQVKPGTI MYDPFAGTGS
2igtB     98    veflgrftaf rhvgvfpeqi vhwe--wlkn avetadrplk vlnlfgytgv
                                                                      
TARGET                                       hhh hhhh    ss sssss    h
2igtB           sssssss           hhh hhhh  hhhh hhhh    ss sssss    h


TARGET    25    FLVAGGHFGS LVIGSDIDGR MIRGKGAQVN ISANFKKYGE SSQFLDVLTM
2igtB     146   aslvaaaaga evthvdaskk aigw------ akenqvlagl eqapirwice
                                                                      
TARGET          hhhhhhhh   ssssss  hh hhh         hhhhhhh      sssss  
2igtB           hhhhhhhh   ssssss  hh hhhh       hhhhhhhh      sssssss


TARGET    75    DFTNN---AL RNNLVIDTIL CDPPYGIRES IKVLGAKDPE RFLGKEDMEI
2igtB     190   daxkfiqree rrgstydiil tdppkfgr-- ----gth-ge ----------
                                                                      
TARGET                            sss s   ssssss sss          sssss  s
2igtB            hhhhhhhhh hh     sss ss  ssss       s    s           


TARGET    122   DGEKAYLRRD YIPTKKPYAL DSLLDDLLQY SSERLPIGGR LAFW -----
2igtB     223   ---------- ------vwql fdhlplxldi creilspkal glvltaysir
                                                                      
TARGET          sssssss    ssssssssss    hhhhhhh hhhh       sss       
2igtB                            ssss    hhhhhhh hhh        ssssss    


TARGET          ---------- ---------- ---------- ---------- ----------
2igtB     257   asfysxhelx retxrgaggv vasgelvire agldgktpgr vlstslfsrw
                                                                      
TARGET                                                                
2igtB              hhhhhhh hhh     ss ssssssssss          s ssssssssss


TARGET          ---                                                   
2igtB     307   epk                                                   
                                                                      
TARGET                                                                
2igtB           s                                                     



Quality


Template's ligands section
Ligands in the template: FMT: 3, GOL: 1, SAM: 1.
Ligands in the template that will be assessed: SAM1002.
Model's ligands section
SAM1002
One or more ligand's atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other ligands.
Given the properties calculated previously, the ligand SAM1002 will not be included in the model.
SAM1002: conservation:False, RMSD:False, included: False

No ligands were included in the model.


Quaternary Structure Annotation of the Template
2igt is annotated as TRIMER
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: 2igt.pdb1.gz

Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 15.385) 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
To build the complex the following chains of the complex has been additionally identified: 2igtA


Template Selection
 - Start SMR-Pipeline for:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Wed Jul 16 16:05:27
2014 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No md5 found in hash for: 3tm5A
FATAL - No md5 found in hash for: 3tm5B
FATAL - No md5 found in hash for: 3tm5A
FATAL - No md5 found in hash for: 3tm4B
FATAL - No md5 found in hash for: 3tm4A
FATAL - No md5 found in hash for: 3tljB
FATAL - No md5 found in hash for: 3tljA
FATAL - No md5 found in hash for: 3vseB
FATAL - No md5 found in hash for: 3vseB
FATAL - No md5 found in hash for: 3vseA
FATAL - No md5 found in hash for: 3vseD
FATAL - No md5 found in hash for: 3vseC
FATAL - No md5 found in hash for: 4l7vA
FATAL - No md5 found in hash for: 4l7vA
FATAL - No md5 found in hash for: 4ku9A
FATAL - No md5 found in hash for: 4ku9A
FATAL - No md5 found in hash for: 4kw7A
FATAL - No md5 found in hash for: 4fr0A
FATAL - No md5 found in hash for: 4fs8A
FATAL - No md5 found in hash for: 4fsdA
FATAL - No md5 found in hash for: 4pcaA
FATAL - No md5 found in hash for: 4pcaA
FATAL - No md5 found in hash for: 4pcaD
FATAL - No md5 found in hash for: 4pcaC
FATAL - No md5 found in hash for: 4pcaB
FATAL - No md5 found in hash for: 4oa8A
FATAL - No md5 found in hash for: 4oa5E
FATAL - No md5 found in hash for: 4pclB
FATAL - No md5 found in hash for: 4pclA
FATAL - No md5 found in hash for: 4oa8B
FATAL - No md5 found in hash for: 4oa5D
FATAL - No md5 found in hash for: 4oa5F
FATAL - No md5 found in hash for: 4oa5A
FATAL - No md5 found in hash for: 4oa5C
FATAL - No md5 found in hash for: 4oa5B
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with D found
 - No template with A found
 - No template with B found
 - No template with C 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 2igtB (199-363) 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 Wed Jul 16 16:06:25
2014 




Template Description
Match Chain SeqId

2igt: CRYSTAL STRUCTURE OF THE SAM DEPENDENT METHYLTRANSFERASE FROM AGROBACTERIUM TUMEFACIENS
Solved by: X-RAY, Resolution: 1.89A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

185-363 2igtC 14%
[Model]
200-363 2igtA 15%
[Model]
199-363 2igtB 15%
[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]
202-367 3hm2G 12%
[Model]
200-367 3hm2E 11%
[Model]
196-367 3hm2F 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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