SWISS-MODEL Repository - Model Details

Model Overview
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1
464

Sequence
UniProt Q91YT0
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q91YT0: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
Complex1_51K
SLBB
NADH_4Fe-4S

Model 3D Structure
Model information:
Modelled residue range: 38 to 445
Based on template: [ 3i9v ]  
Sequence Identity [%]: 46%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3i9v): HETERO OCTAMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: FMN: 1, MN: 1, SF4: 1.
Ligands in the model: SF4: 1
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-01-30. 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                    EDRIFT NLYGRHDWRL KGALRRGDWY KTKE-ILLKG
3i9v1     2     tgpilsgldp rf--ertlya hvgkegswtl dyylrhggye takrvlkekt
                                                                      
TARGET                                         h hhhhh    h hhh       
3i9v1                                          h hhhhh    h hhhhhhh   


TARGET    36    PDWILGEMKT SGLRGRGGAG FPTGLKWSFM NKPSDGRPKY LVVNADEGEP
3i9v1     50    pdevieevkr sglrgrggag fptglkwsfm pk-ddgkqhy licnadesep
                                                                      
TARGET          hhhhhhhhhh   sss      ssshhhhh            s sssss     
3i9v1           hh   hhhhh   sss      ssshhhhh            s sssss     


TARGET    86    GTCKDREIMR HDPHKLVEGC LVGGRAMGAR AAYIYIRGEF YNEASNLQVA
3i9v1     99    gsfkdryile dvphlliegm ilagyairat vgyiyvrgey rraadrleqa
                                                                      
TARGET              hhhhhh    hhhhhhh hhhhhhh  s sssssss    hhhhhhhhhh
3i9v1               hhhhhh    hhhhhhh hhhhhhh  s sssssss    hhhhhhhhhh


TARGET    136   IREAYEAGLI GKNACGSDYD FDVFVVRGAG AYICGEETAL IESIEGKQGK
3i9v1     149   ikearargyl gknlfgtdfs fdlhvhrgag ayicgeetal mnsleglran
                                                                      
TARGET          hhhhhhh                sssssss        hhhhh hhhhh     
3i9v1           hhhhhhh                sssssss        hhhhh hhhhh     


TARGET    186   PRLKPPFPAD VGVFGCPTTV ANVETVAVSP TICRRGGTWF AGFGRERNSG
3i9v1     199   prlkppfpaq sglwgkptti nnvetlasvv pimergadwf aqmgteqskg
                                                                      
TARGET                           ssss s hhhhhhhh hhhh   hhh h sss  sss
3i9v1                            ssss s hhhhhhhh hhhh   hhh h sss  sss


TARGET    236   TKLFNISGHV NHPCTVEEEM SVPLKELIEK HAGGVTGGWD NLLAVIPGGS
3i9v1     249   mklyqisgpv krpgvyelpm gttfreliye waggpl---e piqaiipggs
                                                                      
TARGET          sssssss ss s  sssssss    hhhhhhh hh sss     ssssssss  
3i9v1           sssssss ss s  sssssss    hhhhhhh hh sss     ssssssss  


TARGET    286   STPLIPKSVC E---TVLMDF DALVQAQTGL GTAAVIVMDR STDIVKAIAR
3i9v1     296   stpplpft-- eevldtpmsy ehlqakgsml gtggvilipe rvsmvdamwn
                                                                      
TARGET              sss                            ssssssss    hhhhhhh
3i9v1               sss    hhhh                    ssssssss    hhhhhhh


TARGET    333   LIEFYKHESC GQCTPCREGV -DWMNKVMAR FVKGDARPAE IDSLWEISKQ
3i9v1     344   ltrfyahesc gkctpcregv agfmvnlfak igtgqgeekd venleallpl
                                                                      
TARGET          hhhhhhhh      hhhhh     hhhhhhhh hh      hh hhhhhhhhhh
3i9v1           hhhhhhhh      hhhhhhh hhhhhhhhhh hh      hh hhhhhhh   


TARGET    382   IEGHTICALG DGAAWPVQGL IRHFRPE -- ---------- -----     
3i9v1     394   iegrsfcpla daavwpvkgs lrhfkdqyla larekrpvpr pslwr     
                                                                      
TARGET          hh      hh hhhhhhhhhh h                               
3i9v1           hh      hh hhhhhhh    h    hhhhh hh

Quality 


Template's ligands section 
Ligands in the template: FMN: 1, MN: 1, SF4: 1. 
Ligands in the template that will be assessed: FMN440, MN206, SF4439. 
Model's ligands section 
SF4439 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.070 
Given the properties calculated previously, the ligand 1.SF4439 will be included in the model. 
SF4439: conservation:True, RMSD:True, included: True 
 
FMN440 
Not all the residues interacting with the ligand are completely conserved between model and template. 
No RMSD calculation will be performed. 
Given the properties calculated previously, the ligand 1.FMN440 will not be included in the model. 
FMN440: conservation:False, RMSD:False, included: False 
 
MN206 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand 2.MN206 will not be included in the final model. 
MN206: conservation:False, RMSD:False, included: False 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 3i9v is annotated as HETERO OCTAMER 
 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: 3i9v.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3i9v_1

Template Selection 
 - Start SMR-Pipeline for:96e51eded9464932c820ba059ea4fd31 on BC2-cluster at Fri Feb 22 22:00:31
2013 


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

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with T found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with 2 found
 - No template with 3 found
 - No template with 4 found
 - No template with 5 found
 - No template with 6 found
 - No template with 9 found
 - No template with 7 found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with P found
 - No template with Q found
 - No template with 2 found
 - No template with 3 found
 - No template with 4 found
 - No template with 5 found
 - No template with 6 found
 - No template with 9 found
 - No template with 7 found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with R found
 - No template with H found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with J found
 - No template with O found
 - No template with P found
 - No template with Q found
 - No template with S found
 - No template with T found
 - No template with 2 found
 - No template with 3 found
 - No template with 4 found
 - No template with 5 found
 - No template with 6 found
 - No template with 9 found
 - No template with 7 found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with T found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with 2 found
 - No template with 3 found
 - No template with 4 found
 - No template with 5 found
 - No template with 6 found
 - No template with 9 found
 - No template with 7 found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with P found
 - No template with Q found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with 2 found
 - No template with 3 found
 - No template with 4 found
 - No template with 5 found
 - No template with 6 found
 - No template with 9 found
 - No template with 7 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 3i9v1 (38-445) 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:96e51eded9464932c820ba059ea4fd31 on BC2-cluster at Fri Feb 22 22:02:27
2013

no data available!
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.