SWISS-MODEL Repository - Model Details

Model Overview
Click on the bars to get more details about individual Models or experimental structures
1
889

Sequence
UniProt P28271
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Aconitase
Aconitase_C

Model 3D Structure
Model information:
Modelled residue range: 3 to 889
Based on template: [ 2b3x ]  
Sequence Identity [%]: 93%
Model date: 2013-02-15
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2b3x): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: SF4: 1, ZN: 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        NPFAHLA EPLDAAQPGK RFFNLNKLED SRYGRLPFSI RVLLEAAVRN
2b3xA     2     s--npfahla epldpvqpgk kffnlnkled srygrlpfsi rvlleaairn
                                                                      
TARGET                  ss sss      s ssss hh     hhh   hhh hhhhhhhhhh
2b3xA                   ss s           sss hh     hh    hhh hhhhhhhhhh


TARGET    48    CDEFLVKKND IENILNWNVM QHKNIEVPFK PARVILQDFT GVPAVVDFAA
2b3xA     50    cdeflvkkqd ienilhwnvt qhknievpfk parvilqdft gvpavvdfaa
                                                                      
TARGET                  hh hhhh   hhh hh  sssss    sssssshh hhhhhhhhhh
2b3xA                   hh hhhh   hhh hh  sssss    sssssshh hhhhhhhhhh


TARGET    98    MRDAVKKLGG NPEKINPVCP ADLVIDHSIQ VDFNRRADSL QKNQDLEFER
2b3xA     100   mrdavkklgg dpekinpvcp adlvidhsiq vdfnrradsl qknqdlefer
                                                                      
TARGET          hhhhhhhh            s sssss             hhh hhhhhhhhh 
2b3xA           hhhhhhhh            s sssss             hhh hhhhhhhhh 


TARGET    148   NKERFEFLKW GSQAFCNMRI IPPGSGIIHQ VNLEYLARVV FDQDGCYYPD
2b3xA     150   nrerfeflkw gsqafhnmri ippgsgiihq vnleylarvv fdqdgyyypd
                                                                      
TARGET            hhhhhhhh hhhh  ssss s      hhh hhhh    ss sss  sssss
2b3xA             hhhhhhhh hhhh  ssss s      hhh hhhh    ss sss  sssss


TARGET    198   SLVGTDSHTT MIDGLGVLGW GVGGIEAEAV MLGQPISMVL PQVIGYKLMG
2b3xA     200   slvgtdshtt midglgilgw gvggieaeav mlgqpismvl pqvigyrlmg
                                                                      
TARGET          sssss    h hhhh   sss ss hhhhhhh h    sssss  ssssssss 
2b3xA           sssss    h hhhh   sss ss hhhhhhh h    sssss  ssssssss 


TARGET    248   KPHPLVTSTD IVLTITKHLR QVGVVGKFVE FFGPGVAQLS IADRATIANM
2b3xA     250   kphplvtstd ivltitkhlr qvgvvgkfve ffgpgvaqls iadratianm
                                                                      
TARGET                  hh hhhhhhhhhh hh     sss ss  hhh    hhhhhhhh  
2b3xA                   hh hhhhhhhhhh hh     sss ss  hhh    hhhhhhhh  


TARGET    298   CPEYGATAAF FPVDEVSIAY LLQTGREEDK VKHIQKYLQA VGMFRDFNDT
2b3xA     300   cpeygataaf fpvdevsity lvqtgrdeek lkyikkylqa vgmfrdfndp
                                                                      
TARGET                 sss      hhhhh hhhh   hhh hhhhhhhhhh h         
2b3xA                  sss     hhhhhh hhhh   hhh hhhhhhhhhh h         


TARGET    348   SQDPDFTQVV ELDLKTVVPC CSGPKRPQDK VAVSEMKKDF ESCLGAKQGF
2b3xA     350   sqdpdftqvv eldlktvvpc csgpkrpqdk vavsdmkkdf esclgakqgf
                                                                      
TARGET                 sss ssss    ss ssss    ss sss   hhhh hhhhh     
2b3xA                  sss ssss    ss ssss    ss sss   hhhh hhhhh     


TARGET    398   KGFQVAPDRH NDRKTFLYSN SEFTLAHGSV VIAAITSCTN TSNPSVMLGA
2b3xA     400   kgfqvapehh ndhktfiydn teftlahgsv viaaitsctn tsnpsvmlga
                                                                      
TARGET                        sssss   sssss  sss sssss         hhhhhhh
2b3xA                  hh     sssss   sssss  sss sssss         hhhhhhh


TARGET    448   GLLAKKAVEA GLSVKPYIKT SLSPGSGVVT YYLRESGVMP YLSQLGFDVV
2b3xA     450   gllakkavda glnvmpyikt slspgsgvvt yylqesgvmp ylsqlgfdvv
                                                                      
TARGET          hhhhhhhhhh         ss sss    hhh hhhhh   hh hhhh      
2b3xA           hhhhhhhhhh         ss sss    hhh hhhhh   hh hhhhh     


TARGET    498   GYGCMTCIGN SGPLPEPVVE AITQGDLVAV GVLSGNRNFE GRVHPNTRAN
2b3xA     500   gygcmtcign sgplpepvve aitqgdlvav gvlsgnrnfe grvhpntran
                                                                      
TARGET                          hhhhh hhhh       ssss               ss
2b3xA                           hhhhh hhhh       ssss       hh      ss


TARGET    548   YLASPPLVIA YAIAGTVRID FEKEPLGVNA QGRQVFLKDI WPTRDEIQAV
2b3xA     550   ylaspplvia yaiagtirid fekeplgvna kgqqvflkdi wptrdeiqav
                                                                      
TARGET          sss hhhhhh hhhhsss          sss    sss         hhhhhhh
2b3xA           sss hhhhhh hhhhsss          sss    sss         hhhhhhh


TARGET    598   ERQHVIPGMF KEVYQKIETV NKSWNALAAP SEKLYAWNPK STYIKSPPFF
2b3xA     600   erqyvipgmf kevyqkietv neswnalatp sdklffwnsk styiksppff
                                                                      
TARGET          hhh    hhh hhhh        hhhh                           
2b3xA           hhh    hhh hhhh        hhhh                           


TARGET    648   ESLTLDLQPP KSIVDAYVLL NLGDSVTTDH ISPAGNIARN SPAARYLTNR
2b3xA     650   enltldlqpp ksivdayvll nlgdsvttdh ispagniarn spaaryltnr
                                                                      
TARGET                       sss sss         hhh h           hhhhhhhh 
2b3xA                        sss sss         hhh h           hhhhhhhhh


TARGET    698   GLTPREFNSY GSRRGNDAIM ARGTFANIRL LNKFLNKQAP QTVHLPSGET
2b3xA     700   gltprefnsy gsrrgndavm argtfanirl lnrflnkqap qtihlpsgei
                                                                      
TARGET              hh     h      hhh hhh                 s ssss    ss
2b3xA               hh     h      hhh hhh                    sss    ss


TARGET    748   LDVFDAAERY QQAGLPLIVL AGKEYGSGSS RDWAAKGPFL LGIKAVLAES
2b3xA     750   ldvfdaaery qqaglplivl agkeygagss rdwaakgpfl lgikavlaes
                                                                      
TARGET          ssshhhhhhh hhh  sssss s               hhhhh h  sssss  
2b3xA           s hhhhhhhh hhh  sssss s               hhhhh h  sssss  


TARGET    798   YERIHRSNLV GMGVIPLEYL PGETADSLGL TGRERYTINI PEDLKPRMTV
2b3xA     800   yerihrsnlv gmgvipleyl pgenadalgl tgqerytiii penlkpqmkv
                                                                      
TARGET            hhhhhhhh hh  sssss      hhhh       ssss          sss
2b3xA             hhhhhhhh hh  sssss      hhhh       ssss          sss


TARGET    848   QIKLDTGKTF QAVMRFDTDV ELTYFHNGGI LNYMIRKMAQ           
2b3xA     850   qvkldtgktf qavmrfdtdv eltyflnggi lnymirkmak -         
                                                                      
TARGET          sssss  sss sssss   hh hhhhh   hh hhhhhhhhh            
2b3xA           sssss  sss sssss   hh hhhhh   hh hhhhhhhhh

Quality 


Template's ligands section 
Ligands in the template: SF4: 1, ZN: 1. 
Ligands in the template that will be assessed: SF41000, ZN1001. 
Model's ligands section 
SF41000 
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: 0.060 
Given the properties calculated previously, the ligand A.SF41000 will be included in the model. 
SF41000: conservation:True, RMSD:True, included: True 
 
ZN1001 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand ZN1001 will not be included in the final model. 
ZN1001: conservation:False, RMSD:False, included: False 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 2b3x 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: 2b3x.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 0.296 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:5cce6cfb082cf928f5eed2cc37ce3b1f on BC2-cluster at Fri Feb 15 21:18:16
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 2b3xA (3-889) 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:5cce6cfb082cf928f5eed2cc37ce3b1f on BC2-cluster at Fri Feb 15 21:24:29
2013


Template Description
Match Chain SeqId

2b3y: STRUCTURE OF A MONOCLINIC CRYSTAL FORM OF HUMAN CYTOSOLIC ACONITASE (IRP1)
Solved by: X-RAY, Resolution: 1.85A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-889 2b3yA 93%
[Model]
3-889 2b3yB 93%
[Model]

2b3x: STRUCTURE OF AN ORTHORHOMBIC CRYSTAL FORM OF HUMAN CYTOSOLIC ACONITASE (IRP1)
Solved by: X-RAY, Resolution: 2.54A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-889 2b3xA 93%
[Model]

3snp: CRYSTAL STRUCTURE ANALYSIS OF IRON REGULATORY PROTEIN 1 INWITH FERRITIN H IRE RNA
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-889 3snpA 89%
[Model]
3-889 3snpB 89%
[Model]

3sn2: CRYSTAL STRUCTURE ANALYSIS OF IRON REGULATORY PROTEIN 1 INWITH TRANSFERRIN RECEPTOR IRE B RNA
Solved by: X-RAY, Resolution: 2.99A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-889 3sn2A 88%
[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.