SWISS-MODEL Repository - Model Details

Model Overview
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1
349

Sequence
UniProt P13707
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P13707: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
NAD_Gly3P_dh_N
NAD_Gly3P_dh_C

Model 3D Structure
Model information:
Modelled residue range: 1 to 349
Based on template: [ 1x0v ]  
Sequence Identity [%]: 93%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1x0v): DIMER
Model: DIMER

Ligand information: [details]
Ligands in the template: SO4: 14.
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       AGKKVCIV GSGNWGSAIA KIVGSNAGRL AHFDPRVTMW VFEEDIGGRK
1x0v_1#4  2       askkvciv gsgnwgsaia kivggnaaql aqfdprvtxw vfeediggkk
                                                                      
TARGET               sssss    hhhhhhh hhhhhhhhh        ssss s         
1x0v_1#4             sssss    hhhhhhh hhhhhhhhh        ssss s         


TARGET    49    LTEIINTQHE NVKYLPGHKL PPNVVAIPDV VQAATGADIL VFVVPHQFIG
1x0v_1#4  50    lteiintqhe nvkylpghkl ppnvvavpdv vqaaedadil ifvvphqfig
                                                                      
TARGET          hhhhhhhh                  sss  h hhhhh  sss sss   hhhh
1x0v_1#4        hhhhhhhh                sssss  h hhhhh  sss sss   hhhh


TARGET    99    KICDQLKGHL KANTIGISLI KGVDEGPNGL KLISEVIGER LGIPMSVLMG
1x0v_1#4  100   kicdqlkghl kanatgisli kgvdegpngl kliseviger lgipxsvlxg
                                                                      
TARGET          hhhhhh         sssss               hhhhhhhh h  ssssss 
1x0v_1#4        hhhhhh         sssss               hhhhhhhh h  ssssss 


TARGET    149   ANIASEVAEE KFCETTIGCK DPAQGQLLKD LMQTPNFRIT VVQEVDTVEI
1x0v_1#4  150   aniasevade kfcettigck dpaqgqllke lxqtpnfrit vvqevdtvei
                                                                      
TARGET             hhhhhh    sssssss   hhhhhhhhh h    sssss ss  hhhhhh
1x0v_1#4           hhhhhh    sssssss   hhhhhhhhh hh   sssss ss  hhhhhh


TARGET    199   CGALKNIVAV GAGFCDGLGF GDNTKAAVIR LGLMEMIAFA KLFCSGTVSS
1x0v_1#4  200   cgalknvvav gagfcdglgf gdntkaavir lglxexiafa klfcsgpvss
                                                                      
TARGET          hhhhhhhhhh hhhhhhhh    hhhhhhhhh hhhhhhhhhh hh        
1x0v_1#4        hhhhhhhhhh hhhhhhhh    hhhhhhhhh hhhhhhhhhh hhh       


TARGET    249   ATFLESCGVA DLITTCYGGR NRKVAEAFAR TGKSIEQLEK EMLNGQKLQG
1x0v_1#4  250   atflescgva dlittcyggr nrkvaeafar tgksieqlek ellngqklqg
                                                                      
TARGET          hhh     hh hhhhhh   h hhhhhhhhhh h   hhhhhh h        h
1x0v_1#4        hhh     hh hhhhhh   h hhhhhhhhhh h   hhhhhh h        h


TARGET    299   PQTARELHSI LQHKGLVDKF PLFTAVYKVC YEGQPVGEFI RCLQNHPEHM
1x0v_1#4  300   petarelysi lqhkglvdkf plfxavykvc yegqpvgefi hclqnhpehx
                                                                      
TARGET          hhhhhhhhhh hhhh       hhhhhhhhhh          h hhhh      
1x0v_1#4        hhhhhhhhhh hhhh       hhhhhhhhhh          h hhhh      


TARGET    349    - MAGKKVC IVGSGNWGSA IAKIVGSNAG RLAHFDPRVT MWVFEEDIGG
1x0v_1#4  2     ---xaskkvc ivgsgnwgsa iakivggnaa qlaqfdprvt xwvfeedigg
                 *                                                    
TARGET                 sss ss   hhhhh hhhhhhhhhh h       ss sss       
1x0v_1#4               sss ss   hhhhh hhhhhhhhhh h       ss sss       


TARGET    396   RKLTEIINTQ HENVKYLPGH KLPPNVVAIP DVVQAATGAD ILVFVVPHQF
1x0v_1#4  48    kklteiintq henvkylpgh klppnvvavp dvvqaaedad ilifvvphqf
                                                                      
TARGET            hhhhhhhh                sssss   hhhhhh  s sssss   hh
1x0v_1#4          hhhh   h                sssss   hhhhhh  s sssss   hh


TARGET    446   IGKICDQLKG HLKANTIGIS LIKGVDEGPN GLKLISEVIG ERLGIPMSVL
1x0v_1#4  98    igkicdqlkg hlkanatgis likgvdegpn glklisevig erlgipxsvl
                                                                      
TARGET          hhhhhh           ssss s    sss   sss hhhhhh hhh  sssss
1x0v_1#4        hhhh   h         ssss s    sss   sss hhhhhh hhh  sssss


TARGET    496   MGANIASEVA EEKFCETTIG CKDPAQGQLL KDLMQTPNFR ITVVQEVDTV
1x0v_1#4  149   xganiaseva dekfcettig ckdpaqgqll kelxqtpnfr itvvqevdtv
                                                                      
TARGET          s    hhhhh h   ssssss s  hhhhhhh hhh    sss ssss  hhhh
1x0v_1#4        s    hhhhh h   ssssss s  hhhhhhh hhhh   sss ssss  hhhh


TARGET    546   EICGALKNIV AVGAGFCDGL GFGDNTKAAV IRLGLMEMIA FAKLFCSGTV
1x0v_1#4  198   eicgalknvv avgagfcdgl gfgdntkaav irlglxexia faklfcsgpv
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh    hhhhhhh hhhhhhhhhh hhhhh     
1x0v_1#4        hhhhhhhhhh hhhhhhhhhh    hhhhhhh hhhhhhhhhh hhhhh     


TARGET    596   SSATFLESCG VADLITTCYG GRNRKVAEAF ARTGKSIEQL EKEMLNGQKL
1x0v_1#4  248   ssatflescg vadlittcyg grnrkvaeaf artgksieql ekellngqkl
                                                                      
TARGET            hhh      hhhhhhhh    hhhhhhhhh hh    hhhh hhh       
1x0v_1#4          hhh      hhhhhhhh    hhhhhhhhh hh    hhhh hhh       


TARGET    646   QGPQTARELH SILQHKGLVD KFPLFTAVYK VCYEGQPVGE FIRCLQNHPE
1x0v_1#4  298   qgpetarely silqhkglvd kfplfxavyk vcyegqpvge fihclqnhpe
                                                                      
TARGET           hhhhhhhhh hhhh   hhh    hhhhhhh hh          hhhh     
1x0v_1#4         hhhhhhhhh hhhh   hh    hhhhhhhh hh          hhhh     


TARGET    696   HM                                                    
1x0v_1#4  348   hx-                                                   
                                                                      
TARGET                                                                
1x0v_1#4

Quality 


Template's ligands section 
Ligands in the template: SO4: 14. 
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 
 1x0v 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: 1x0v.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 0.902 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 1x0vA  
 Model was succesfully built as DIMER.

Template Selection 
 - Start SMR-Pipeline for:07655ca9cf3927c7cd6fc774e8f68ca6 on BC2-cluster at Sat Feb 23 05:21:00
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 1x0vB (1-349) 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:07655ca9cf3927c7cd6fc774e8f68ca6 on BC2-cluster at Sat Feb 23 05:23:46
2013


Template Description
Match Chain SeqId

1x0x: CO-STRUCTURE OF HOMO SAPIENS GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1 COMPLEX WITH NAD
Solved by: X-RAY, Resolution: 2.75A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-349 1x0xA 94%
[Model]

1wpq: TERNARY COMPLEX OF GLYCEROL 3-PHOSPHATE DEHYDROGENASE 1 WITH NAD AND DIHYDROXYACTONE
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-349 1wpqA 94%
[Model]
2-349 1wpqB 94%
[Model]

1x0v: CRYSTAL STRUCTURE OF HOMO SAPIEN GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-349 1x0vB 94%
[Model]
2-349 1x0vA 94%
[Model]

2pla: CRYSTAL STRUCTURE OF HUMAN GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1-LIKE PROTEIN
Solved by: X-RAY, Resolution: 2.51A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

5-344 2plaA 72%
[Model]
5-344 2plaB 72%
[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.