SWISS-MODEL Repository - Model Details

Model Overview
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1
447

Sequence
UniProt Q3EBM5
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Asp

Model 3D Structure
Model information:
Modelled residue range: 84 to 438
Based on template: [ 3vlb ]  
Sequence Identity [%]: 24%
Model date: 2013-02-19
Revision date: 2013-01-30

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

Ligand information: [details]
Ligands in the template: none.
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                        EF FMSITIGTPP IKVFAIADTG SDLTWVQCKP
3vlbC     5     rpsalvvpvk kdastl--qy vttinqrtpl vsenlvvdlg grflwvdc--
                                                                      
TARGET                              s sssssss  s ssssssss     ssssss  
3vlbC             ssssssss ss      ss sssssss  s ssssssss   ssssssss  


TARGET    33    CQQCYKENGP IFDKKKSSTY KSEPCDSRNC QALSSTE--- -RGCDESNNI
3vlbC     51    -dqnyv---- ------ssty rpvrcrtsqc slsgsiacgd cfgcn--nnt
                                                                      
TARGET                ssss   ssss     sss    hhh h                    
3vlbC                                 sss    hhh h                    


TARGET    79    CKYR-YSYGD QSFSKGDVAT ETVSIDSASG SP----VSFP GTVFGCGYNN
3vlbC     93    cgvfpenpvi ntatggevae dvvsvestdg sssgrvvtvp rfifscapts
                                                                      
TARGET                           ssss sssssss    ss    ssss  ssssss   
3vlbC             ssssss   ssssssssss ssssssss       ssssss  ssssss  h


TARGET    124   GGTFDETGSG IIGLGG---G HLSLISQLGS SISK--KFSY CLSHKSATTN
3vlbC     143   --llqnlasg vvgmaglgrt rialpsqfas afsfkrkfam cl---sgsts
                                                                      
TARGET                      sssss        hhhhhh                       
3vlbC             h         sssssss      hhhhhhh hh   sssss s         


TARGET    169   GTSVINLGTN SIPS---SLS KDSGVVSTPL VDKEP----- ------LTYY
3vlbC     188   snsviifgnd pytflpniiv sdktltytpl ltnpvstsat stqgepsvey
                                                                      
TARGET                                     sssss                     s
3vlbC             sssssss   sss   sss      sssss                     s


TARGET    205   YLTLEAISVG KKKIPYTGSS YNPNDDGILS ETSGNIIIDS GTTLTLLEAG
3vlbC     238   figvksikin skivalntsl lsissagl-- ---ggtkist inpytvlets
                                                                      
TARGET          ss   sssss  sss                       sss    sss     h
3vlbC           ss   sssss  sss                      sssss      sss  h


TARGET    255   FFDKFSS--A VEESVTGAKR VSDPQGLLSH CFK---SGSA EIG--LPEIT
3vlbC     283   iykavteafi kesaarnitr vas-vapfga cfstdnilst rlgpsvpsid
                                                                      
TARGET          hhhhh       hhh    ss s        s sss               sss
3vlbC           hhhhhhhhhh hhhh    ss s        s ssss   sss   sss  sss


TARGET    298   VHFTGADVR- -LSPINAFVK LSEDMVCLSM VPT-----TE VAIYGNFAQM
3vlbC     332   lvlqsesvvw titgsnsmvy indnvvclgv vdggsnlrts ivigghqle-
                                                                      
TARGET          ss            h  ssss s   sssssh hhh     hh h sss     
3vlbC           sss    sss ss hhhsss     ssssss  sss        sss       


TARGET    341   DFLVGYDLET RTVSF ---- ---------- --                   
3vlbC     381   dnlvqfdlat srvgfsgtll gsrttcanfn ft                   
                                                                      
TARGET            sssss    sssss                                      
3vlbC             ssssss   ssssss   h hh

Quality 


Template's ligands section 
Template without ligands. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3vlb is annotated as HETERO 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: 3vlb.pdb2.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3vlb_2

Template Selection 
 - Start SMR-Pipeline for:f33c5e53654628c6c15d53625c6fe94c on BC2-cluster at Tue Feb 19 15:03:37
2013 


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

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with D found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B 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 3vlbC (84-438) 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:f33c5e53654628c6c15d53625c6fe94c on BC2-cluster at Tue Feb 19 15:07:00
2013


Template Description
Match Chain SeqId

4aa9: CAMEL CHYMOSIN AT 1.6A RESOLUTION
Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

80-441 4aa9A 17%
[Model]

4cms: X-RAY ANALYSES OF ASPARTIC PROTEINASES IV. STRUCTURE AND REFINEMENT AT 2.2 ANGSTROMS RESOLUTION OF BOVINE CHYMOSIN
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

80-441 4cmsA 15%
[Model]

1cms: THE THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT BOVINE CHYMOSIN AT 2.3 ANGSTROMS RESOLUTION
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

80-441 1cmsA 15%
[Model]

3cms: ENGINEERING ENZYME SUB-SITE SPECIFICITY: PREPARATION, KINETIC CHARACTERIZATION AND X-RAY ANALYSIS AT 2.0- ANGSTROMS RESOLUTION OF VAL111PHE SITE-MUTATED CALF CHYMOSIN
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

80-441 3cmsA 15%
[Model]

4aa8: BOVINE CHYMOSIN AT 1.8A RESOLUTION
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

80-441 4aa8A 15%
[Model]

1czi: CHYMOSIN COMPLEX WITH THE INHIBITOR CP-113972
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

80-441 1cziE 15%
[Model]

3vv6: CRYSTAL STRUCTURE OF BETA SECETASE IN COMPLEX WITH 2-AMINO((1S, 2R)-2-PHENYLCYCLOPROPYL)PYRIMIDIN-4(3H)-ONE
Solved by: X-RAY, Resolution: 2.05A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

76-445 3vv6A 14%
[Model]

2zjl: CRYSTAL STRUCTURE OF THE HUMAN BACE1 CATALYTIC DOMAIN IN COMPLEX WITH N-[1-(5-BROMO-2,3-DIMETHOXY-BENZYL)-PIPERIDI4-YL]-4-MERCAPTO-BUTYRAMIDE
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-445 2zjlA 14%
[Model]

3bug: BACE-1 COMPLEXED WITH COMPOUND 3
Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

80-446 3bugA 14%
[Model]

3vv8: CRYSTAL STRUCTURE OF BETA SECETASE IN COMPLEX WITH 2-AMINO((1S,2R)-2-(3'-METHYLBIPHENYL-4-YL)CYCLOPROPYL)PYRIMIDIN-
Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-445 3vv8A 14%
[Model]

3buf: BACE-1 COMPLEXED WITH COMPOUND 2
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

76-446 3bufA 14%
[Model]

3kyr: BACE-1 IN COMPLEX WITH A NORSTATINE TYPE INHIBITOR
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-445 3kyrC 14%
[Model]

2zjh: CRYSTAL STRUCTURE OF THE HUMAN BACE1 CATALYTIC DOMAIN IN COMPLEX WITH N-(1-BENZYL-PIPERIDIN-4-YL)-4-MERCAPTO- BUTYRAMIDE
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-445 2zjhA 13%
[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.