SWISS-MODEL Repository - Model Details

Model Overview
Click on the bars to get more details about individual Models or experimental structures
1
520

Sequence
UniProt Q9D0K2
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9D0K2: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
CoA_trans
CoA_trans

Model 3D Structure
Model information:
Modelled residue range: 40 to 519
Based on template: [ 3dlx ]  
Sequence Identity [%]: 92%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3dlx): DIMER
Model: DIMER

Ligand information: [details]
Ligands in the template: GOL: 1.
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 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       TKFYTDPV EAVKDIPNGA TLLVGGFGLC GIPENLIGAL LKTGVKDLTA
3dlx_1#4  40      tkfytdpv eavkdipdga tvlvggfglc gipenlidal lktgvkglta
                                                                      
TARGET             sss  hh h        s sssss         hhhhhhh hhh    sss
3dlx_1#4           sss   h h        s sssss         hhhhhhh hhh    sss


TARGET    49    VSNNAGVDNF GLGLLLRSKQ IKRMISSYVG ENAEFERQFL SGELEVELTP
3dlx_1#4  88    vsnnagvdnf glglllrskq ikrmvssyvg enaeferqyl sgeleveltp
                                                                      
TARGET          ss           hhhhhh    ssssssss    hhhhhhhh h   sssss 
3dlx_1#4        ss           hhhhhh    ssssssss    hhhhhhhh h   sssss 


TARGET    99    QGTLAERIRA GGAGVPAFYT STGYGTLVQE GGSPIKYNKD GSVAIASKPR
3dlx_1#4  138   qgtlaerira ggagvpafyt ptgygtlvqe ggspikynkd gsvaiaskpr
                                                                      
TARGET          hhhhhhhhhh hhh  sssss       hhhh   ssssss    ssssss   
3dlx_1#4        hhhhhhhhhh hhh  sssss       hhhh   ssssss    ssssss   


TARGET    149   EVREFNGQHF ILEEAITGDF ALVKAWKADR AGNVIFRKSA RNFNLPMCKA
3dlx_1#4  188   evrefngqhf ileeaitgdf alvkawkadr agnvifrksa rnfnlpmcka
                                                                      
TARGET          sssss  sss sssss   ss sssss ssss   sss         hhhhh  
3dlx_1#4        sssss  sss sssss   ss sssss ssss   sss         hhhhh  


TARGET    199   AGTTVVEVEE IVDIGSFAPE DIHIPKIYVH RLIKGEKYEK RIERLSLRKE
3dlx_1#4  238   aettvvevee ivdigafape dihipqiyvh rlikgekyek rierlsir--
                                                                      
TARGET            ssssss s ss                  s sssss             hh 
3dlx_1#4          ssssss s ss                  s sssss                


TARGET    249   GDGKGKSGKP GGDVRERIIK RAALEFEDGM YANLGIGIPL LASNFISPNM
3dlx_1#4  286   --------kp gddvreriik raalefedgm yanlgigipl lasnfispni
                                                                      
TARGET            hhhhhhh    hhhhhhhh hhhh     s sssss   hh hhhhh     
3dlx_1#4                     hhhhhhhh hhhh     s sssss   hh hhhhh     


TARGET    299   TVHLQSENGV LGLGPYPLKD EADADLINAG KETVTVLPGA SFFSSDESFA
3dlx_1#4  338   tvhlqsengv lglgpyprqh eadadlinag ketvtilpga sffssdesfa
                                                                      
TARGET            ssss  ss ssss            sss    ssssss    sss hhhhhh
3dlx_1#4          ssss  ss ssss            sss    ssssss    sss hhhhhh


TARGET    349   MIRGGHVNLT MLGAMQVSKY GDLANWMIPG KMVKGMGGAM DLVSSSKTKV
3dlx_1#4  388   mirgghvdlt mlgamqvsky gdlanwmipg kmvkgmggam dlvssaktkv
                                                                      
TARGET          hhh    sss ss   ssss   sss          sss  hh h       ss
3dlx_1#4        hhh    sss ss   ssss   sss          sss  hh hhh     ss


TARGET    399   VVTMEHSAKG NAHKIMEKCT LPLTGKQCVN RIITEKGVFD VDKKNGLTLI
3dlx_1#4  438   vvtmehsakg nahkimekct lpltgkqcvn riitekavfd vdkkkgltli
                                                                      
TARGET          ssss          sss              s ssss sssss ss   sssss
3dlx_1#4        ssss          sss              s ssss sssss ss   sssss


TARGET    449   ELWEGLTVDD IKKSTGCDFA VSPNLMPMQQ IS - TKFYT DPVEAVKDIP
3dlx_1#4  488   elwegltvdd vqkstgcdfa vspklmpmqq ia---tkfyt dpveavkdip
                                                    *                 
TARGET          sss     hh hh       s ss   sss         sss   hhh      
3dlx_1#4        sss     hh hh       s ss   sss         sss   hhh      


TARGET    496   NGATLLVGGF GLCGIPENLI GALLKTGVKD LTAVSNNAGV DNFGLGLLLR
3dlx_1#4  55    dgatvlvggf glcgipenli dallktgvkg ltavsnnagv dnfglglllr
                                                                      
TARGET            ssssss         hhhh hhhhhh     sssss           hhhhh
3dlx_1#4          ssssss         hhhh hhhhhh      ssss           hhhhh


TARGET    546   SKQIKRMISS YVGENAEFER QFLSGELEVE LTPQGTLAER IRAGGAGVPA
3dlx_1#4  105   skqikrmvss yvgenaefer qylsgeleve ltpqgtlaer iraggagvpa
                                                                      
TARGET              ssssss ss    hhhh hhhh   sss ss hhhhhhh hhhhhh  ss
3dlx_1#4        h   ssssss ss    hhhh hhhh   sss ss hhhhhhh hhhhhh  ss


TARGET    596   FYTSTGYGTL VQEGGSPIKY NKDGSVAIAS KPREVREFNG QHFILEEAIT
3dlx_1#4  155   fytptgygtl vqeggspiky nkdgsvaias kprevrefng qhfileeait
                                                                      
TARGET          sss      h hhh  sssss s   ssssss    sssss   ssssssss  
3dlx_1#4        sss      h hhh  sssss s   ssssss    sssss   ssssssss  


TARGET    646   GDFALVKAWK ADRAGNVIFR KSARNFNLPM CKAAGTTVVE VEEIVDIGSF
3dlx_1#4  205   gdfalvkawk adragnvifr ksarnfnlpm ckaaettvve veeivdigaf
                                                                      
TARGET           sssssss s sss  sss         hhhh h    sssss s sss     
3dlx_1#4         sssssss s sss  sss         hhhh h    sssss s sss     


TARGET    696   APEDIHIPKI YVHRLIKGEK YEKRIERLSL RKEGDGKGKS GKPGGDVRER
3dlx_1#4  255   apedihipqi yvhrlikgek yekrierlsi rd-------- -----dvrer
                                                                      
TARGET                       ssssss               hhhhhhhhh hhh   hhhh
3dlx_1#4                     ssssss                              hhhhh


TARGET    746   IIKRAALEFE DGMYANLGIG IPLLASNFIS PNMTVHLQSE NGVLGLGPYP
3dlx_1#4  305   iikraalefe dgmyanlgig ipllasnfis pnitvhlqse ngvlglgpyp
                                                                      
TARGET          hhhhhhh      ssssss   hhhhhhh         ssss   ssssss   
3dlx_1#4        hhhhhhh      ssssss   hhhhhhh         ssss   ssssss   


TARGET    796   LKDEADADLI NAGKETVTVL PGASFFSSDE SFAMIRGGHV NLTMLGAMQV
3dlx_1#4  355   rqheadadli nagketvtil pgasffssde sfamirgghv dltmlgamqv
                                                                      
TARGET                  ss s   ssssss    sss hhh hhhhhh     sssss   ss
3dlx_1#4                ss s   ssssss    sss hhh hhhhhh     sssss   ss


TARGET    846   SKYGDLANWM IPGKMVKGMG GAMDLVSSSK TKVVVTMEHS AKGNAHKIME
3dlx_1#4  405   skygdlanwm ipgk-vkgmg gamdlvssak tkvvvtmehs akgnahkime
                                                                      
TARGET          ss  sss          sss   hhhhh      ssssss          sss 
3dlx_1#4        ss  sss          sss   hhhhh      ssssss          sss 


TARGET    896   KCTLPLTGKQ CVNRIITEKG VFDVDKKNGL TLIELWEGLT VDDIKKSTGC
3dlx_1#4  455   kctlpltgkq cvnriiteka vfdvdkkkgl tlielweglt vddvqkstgc
                                                                      
TARGET                       sssss ss sssss   ss ssssss     hhhhh     
3dlx_1#4                     sssss ss sssss   ss ssssss     hhhhhhh   


TARGET    946   DFAVSPNLMP MQQI                                       
3dlx_1#4  505   dfavspklmp mqqi-                                      
                                                                      
TARGET            sss                                                 
3dlx_1#4          sss

Quality 


Template's ligands section 
Ligands in the template: 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 
 3dlx 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: 3dlx.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=DIMER) 
 The corresponding reliability score is 0.86 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 3dlxB  
 Model was succesfully built as DIMER.

Template Selection 
 - Start SMR-Pipeline for:86e65cf3bee4a37235a84d88d5af197f on BC2-cluster at Fri Feb 22 12:33:47
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

FATAL - No A3m found

 - 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 3dlxA (40-519) 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:86e65cf3bee4a37235a84d88d5af197f on BC2-cluster at Fri Feb 22 12:42:53
2013


Template Description
Match Chain SeqId

1m3e: SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM PIG HEART (SELENOMETHIONINE)
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-520 1m3eB 92%
[Model]
40-520 1m3eA 92%
[Model]
40-520 1m3eC 92%
[Model]
40-520 1m3eD 92%
[Model]

3dlx: CRYSTAL STRUCTURE OF HUMAN 3-OXOACID COA TRANSFERASE 1
Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-519 3dlxA 93%
[Model]
40-518 3dlxB 92%
[Model]
40-519 3dlxC 92%
[Model]
40-519 3dlxD 91%
[Model]

2nrb: C28S MUTANT OF SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROPIG HEART
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-519 2nrbB 92%
[Model]
40-519 2nrbA 91%
[Model]
40-519 2nrbD 91%
[Model]
40-519 2nrbC 91%
[Model]

1ooy: SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM PIG HEART
Solved by: X-RAY, Resolution: 1.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-520 1ooyB 92%
[Model]
40-520 1ooyA 91%
[Model]

2nrc: C28A MUTANT OF SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROPIG HEART
Solved by: X-RAY, Resolution: 2.05A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-519 2nrcB 92%
[Model]
40-519 2nrcA 91%
[Model]
40-519 2nrcD 91%
[Model]
40-519 2nrcC 91%
[Model]

3k6m: DYNAMIC DOMAINS OF SUCCINYL-COA:3-KETOACID-COENZYME A TRANPIG HEART.
Solved by: X-RAY, Resolution: 1.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-519 3k6mA 91%
[Model]
40-519 3k6mB 90%
[Model]
40-519 3k6mC 91%
[Model]
40-519 3k6mD 91%
[Model]

1ooz: DELETION MUTANT OF SUCCINYL-COA:3-KETOACID COA TRANSFERASEFROM PIG HEART
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-520 1oozA 90%
[Model]
40-520 1oozB 90%
[Model]

3oxo: SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM PIG HEART COVBOUND TO COA
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-518 3oxoA 92%
[Model]
40-518 3oxoB 92%
[Model]
40-518 3oxoD 91%
[Model]
40-518 3oxoC 91%
[Model]
40-518 3oxoF 91%
[Model]
40-518 3oxoE 91%
[Model]
40-518 3oxoG 90%
[Model]
40-518 3oxoH 90%
[Model]

1ope: DELETION MUTANT OF SUCCINYL-COA:3-KETOACID COA TRANSFERASEFROM PIG HEART
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-520 1opeB 91%
[Model]
40-520 1opeA 89%
[Model]

1o9l: SUCCINATE:COENZYME-A TRANSFERASE (PIG HEART)
Solved by: X-RAY, Resolution: 2.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

40-520 1o9lA 91%
[Model]
40-520 1o9lD 91%
[Model]
40-520 1o9lC 83%
[Model]
40-520 1o9lB 83%
[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.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.