SWISS-MODEL Repository - Model Details

Model Overview
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1
481

Sequence
UniProt P41572
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
6PGD
NAD_binding_2

Model 3D Structure
Model information:
Modelled residue range: 3 to 468
Based on template: [ 4gwg ]  
Sequence Identity [%]: 72%
Model date: 2013-05-07
Revision date: 2013-04-01

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

Ligand information: [details]
Ligands in the template: MES: 2.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment 

TARGET    1       GQADIALI GLAVMGQNLI LNMDEKGFVV CAYNRTVAKV KEFLANEAKD
4gwgA     1       aqadiali glavmgqnli lnmndhgfvv cafnrtvskv ddflaneakg
                                                                      
TARGET                ssss s  hhhhhhh hhhhh    s sss    hhh hhhhh     
4gwgA                 ssss s  hhhhhhh hhhhh    s sss    hhh hhhhh     


TARGET    49    TKVIGADSLE DMVSKLKSPR KVMLLVKAGS AVDDFIQQLV PLLSAGDVII
4gwgA     49    tkvvgaqslk emvsklkkpr riillvkagq avddfieklv plldtgdiii
                                                                      
TARGET             sss  hh hhhh     s sssss      hhhhhhhhhh hh    ssss
4gwgA              sss  hh hhhh     s sssss      hhhhhhhhhh hh    ssss


TARGET    99    DGGNSEYQDT SRRCDELAKL GLLFVGSGVS GGEEGARHGP SLMPGGHEAA
4gwgA     99    dggnseyrdt trrcrdlkak gilfvgsgvs ggeegarygp slmpggnkea
                                                                      
TARGET          ss    hhhh hhhhhhhhhh   ssssssss   hhhhh    sssssss hh
4gwgA           ss    hhhh hhhhhhhhhh   ssssssss   hhhhh    sssssss hh


TARGET    149   WPLIQPIFQA ICAKA-DGEP CCEWVGDGGA GHFVKMVHNG IEYGDMQLIC
4gwgA     149   wphiktifqg iaakvgtgep ccdwvgdega ghfvkmvhng ieygdmqlic
                                                                      
TARGET          hhhhhhhhhh h sss   ss s        h hhhhhhhhhh hhhhhhhhhh
4gwgA           hhhhhhhhhh h sss   ss s        h hhhhhhhhhh hhhhhhhhhh


TARGET    198   EAYHIMKSLG -LSADQMADE FGKWNSAELD SFLIEITRDI LKYKDGK-GY
4gwgA     199   eayhlmkdvl gmaqdemaqa fedwnkteld sflieitani lkfqdtdgkh
                                                                      
TARGET          hhhhhhhh      hhhhhhh hhhhh       hhhhhhhhh hh        
4gwgA           hhhhhhhhh     hhhhhhh hhhhh       hhhhhhhhh hh        


TARGET    246   LLERIRDTAG QKGTGKWTAI AALQYGVPVT LIGEAVFSRC LSALKDERVQ
4gwgA     249   llpkirdsag qkgtgkwtai saleygvpvt ligeavfarc lsslkderiq
                                                                      
TARGET           hh            hhhhhh hhhhh      hhhhhhhhhh hh   hhhhh
4gwgA            hh            hhhhhh hhhhh    h hhhhhhhhhh hh   hhhhh


TARGET    296   ASSVLKGPST KAQVANLTKF LDDIKHALYC AKIVSYAQGF MLMREAAREN
4gwgA     299   askklkgpfq fd--gdkksf ledirkalya skiisyaqgf mllrqaatef
                                                                      
TARGET          hh               hhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh
4gwgA           hh               hhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    346   KWRLNYGGIA LMWRGGCIIR SVFLGNIKDA YTSQPELSNL LLDDFFKKAI
4gwgA     349   gwtlnyggia lmwrggciir svflgkikda fdrnpelqnl llddffksav
                                                                      
TARGET               hhhhh hh           hhhhhhhh hhh           hhhhhhh
4gwgA                hhhhh hh           hhhhhhhh hhh           hhhhhhh


TARGET    396   ERGQDSWREV VANAFRWGIP VPALSTALSF YDGYRTAKLP ANLLQAQRDY
4gwgA     399   encqdswrra vstgvqagip mpcfttalsf ydgyrhemlp asliqaqrdy
                                                                      
TARGET          hhhhhhhhhh hhhhhhh     hhhhhhhhh hhhh       hhhhhhhhhh
4gwgA           hhhhhhhhhh hhhhhhh     hhhhhhhhh hhhh       hhhhhhhhhh


TARGET    446   FGAHTYELLG QEGQFHHTNW T                               
4gwgA     449   fgahtyella kpgqfihtnw t-                              
                                                                      
TARGET          h                                                     
4gwgA           h

Quality 


Template's ligands section 
Ligands in the template: MES: 2. 
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 
 4gwg 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: 4gwg.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.258 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:58f72cfc63ed371a202fe703ef3fa453 on BC2-cluster at Tue May  7 11:08:01
2013 


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

 - 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 4gwgA (3-468) 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:58f72cfc63ed371a202fe703ef3fa453 on BC2-cluster at Tue May  7 11:11:16
2013


Template Description
Match Chain SeqId

1pgn: CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANIS
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-472 1pgnA 72%
[Model]

2pgd: THE STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE REFINED AT 2 ANGSTROMS RESOLUTION
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-472 2pgdA 72%
[Model]

4gwg: CRYSTAL STRUCTURE ANALYSIS OF 6-PHOSPHOGLUCONATE DEHYDROGEFORM
Solved by: X-RAY, Resolution: 1.39A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-468 4gwgA 72%
[Model]

2jkv: STRUCTURE OF HUMAN PHOSPHOGLUCONATE DEHYDROGENASE IN COMPLEX WITH NADPH AT 2.53A
Solved by: X-RAY, Resolution: 2.53A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-481 2jkvB 72%
[Model]
3-481 2jkvA 72%
[Model]
3-481 2jkvD 72%
[Model]
3-481 2jkvC 72%
[Model]
3-481 2jkvE 72%
[Model]
3-469 2jkvF 72%
[Model]

1pgo: CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANIS
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-472 1pgoA 72%
[Model]

1pgq: CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANIS
Solved by: X-RAY, Resolution: 3.17A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-472 1pgqA 72%
[Model]

4gwk: CRYSTAL STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE COMP3-PHOSPHOGLYCERIC ACID
Solved by: X-RAY, Resolution: 1.53A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-468 4gwkA 72%
[Model]

1pgp: CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANIS
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-472 1pgpA 72%
[Model]

2p4q: CRYSTAL STRUCTURE ANALYSIS OF GND1 IN SACCHAROMYCES CEREVISIAE
Solved by: X-RAY, Resolution: 2.37A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

5-468 2p4qA 66%
[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.