SWISS-MODEL Repository - Model Details

Model Overview
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1
409

Sequence
UniProt Q8JZV7
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q8JZV7: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
Amidohydro_1

Model 3D Structure
Model information:
Modelled residue range: 54 to 403
Based on template: [ 1yrr ]  
Sequence Identity [%]: 34%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1yrr): TETRAMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: GOL: 3, PO4: 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                                                    EQRDCGG
1yrrA     1     myaltqgrif tgheflddha vviadgliks vcpvaelppe i--eqrslng
                                                                      
TARGET                                                                
1yrrA            ssss  sss s  sss sss ssss sssss ssss          sssss  


TARGET    8     RILAPGFIDV QINGGFGVDF SKATEDVG-S GVALVARRLL SHGVTSFCPT
1yrrA     49    ailspgfidv qlngcggvqf ndtaeavsve tleimqkane ksgctnylpt
                                                                      
TARGET           ssssssss    ssss sss             hhhhhhhhh      sssss
1yrrA           sssssssss    sss  sss         hh hhhhhhhhhh      sssss


TARGET    57    LVTSPPEVYH KVLPQIPVKS GGPHGAGVLG VHLEGPFISR EKRGAHPEAY
1yrrA     99    littsdelmk qgv-rvmrey lakhpnqalg lhlegpwlnl vkkthnpn-f
                                                                      
TARGET          sss  hhhhh       hhhh hhh        ssss                 
1yrrA           sss  hhhhh hhh hhhhhh hhh        ssss                 


TARGET    107   LRSFEANAFH DVLATYGPLD NVCIVTLAPE LDRSHEVIQA LTAQGIRVSL
1yrrA     148   vrkpda-alv dflcena--d vitkvtlape mvpa-evisk lanagivvsa
                                                                      
TARGET                   h hhhhhh       sssss           hhh hhh   ssss
1yrrA             hhhh hhh hhhhh        sssss         hhhhh hhh   ssss


TARGET    157   GHSVADLRAA EVAVQSGATF ITHLFNAMLP FHHRDPGIVG LLTSDQLPPG
1yrrA     194   ghsnatlkea kagfragitf athlynampy itgrepglag aildea----
                                                                      
TARGET          s     hhhh hhhhhh  ss s                 hhh hhhh      
1yrrA           s     hhhh hhhhhh  ss s                 hhh hhhh      


TARGET    207   HCIFYGMIAD GIHTNPAALR IAHRAHPQGL VLVTDAVPAL GLGNGRHTLG
1yrrA     240   -diycgiiad glhvdyanir nakrlkgdkl clvtdatapa ganieqfifa
                                                                      
TARGET             ssss         hhhhh hhhhh   ss sss  sss       sssss 
1yrrA              ssss         hhhhh hhhhhh  ss sss            sssss 


TARGET    257   QQEVE-VDGL IAYIAGTKTL GGSIAPMDVC VRHFLQATGC SVESALEAAS
1yrrA     289   gktiyyrngl cvdeng--tl sgssltmieg vrnlvehcgi aldevlrmat
                                                                      
TARGET           ssss ss s sssss ssss s     hhhh hhhhhh      hhhhhh   
1yrrA            ssssss  s sss     ss s     hhhh hhhhhh      hhhhhh   


TARGET    306   LHPAQMLGLE KTKGSLDFGA DADFVVLDDT LHVQATYI-S GELVWQ    
1yrrA     337   lyparaigve krlgtlaagk vanltaftpd fkitktivng nevvtq-   
                                                                      
TARGET          hhhhhhh                 ssssss    sssssss   ssssss    
1yrrA           hhhhh   hh hh       s ssssssss    ssssssss  ssssss    



Quality


Template's ligands section
Ligands in the template: GOL: 3, PO4: 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
1yrr is annotated as TETRAMER
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: 1yrr.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 (=TETRAMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.008 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1yrrB


Template Selection
 - Start SMR-Pipeline for:6b3d970e9f5dc13fbc1cf8efc0ceb52c on BC2-cluster at Fri Feb 22 17:21:11
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 A found
 - No template with D found
 - No template with G found
 - No template with J found
 - No template with M found
 - No template with P found
 - No template with A found
 - No template with D found
 - No template with G found
 - No template with J found
 - No template with M found
 - No template with P found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with D found
 - No template with G found
 - No template with J found
 - No template with M found
 - No template with P found
 - No template with A found
 - No template with D found
 - No template with G found
 - No template with J found
 - No template with M found
 - No template with P found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with A found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -             ********************************************************************
 - building model based on 2vhlA (62-407) was not successful go to next best template
 -             ********************************************************************
 - building model based on 2vhlB (62-407) was not successful go to next best template
 -            ********************************************************************
 - building model based on 1yrrA (54-403) was successful 
 -    ***************************************************************************
 - building model based on 3iv8A (15-399) 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:6b3d970e9f5dc13fbc1cf8efc0ceb52c on BC2-cluster at Fri Feb 22 17:27:21
2013 




Template Description
Match Chain SeqId

1e9z: CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

4-108 1e9zB 17%
[Model]

1e9y: CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE IN COMPLEXWITH ACETOHYDROXAMIC ACID
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

5-108 1e9yB 17%
[Model]

3qgk: 3.0 A MODEL OF IRON CONTAINING UREASE UREA2B2 FROM HELICOBMUSTELAE (REFINED W/ NO ORDERED SOLVENT)
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-109 3qgkL 17%
[Model]
3-109 3qgkO 17%
[Model]
3-109 3qgkR 17%
[Model]
3-109 3qgkC 17%
[Model]
3-109 3qgkF 17%
[Model]
3-109 3qgkI 17%
[Model]

3qga: 3.0 A MODEL OF IRON CONTAINING UREASE UREA2B2 FROM HELICOBMUSTELAE
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-109 3qgaO 17%
[Model]
3-109 3qgaR 17%
[Model]
3-109 3qgaC 17%
[Model]
3-109 3qgaF 17%
[Model]
3-109 3qgaI 17%
[Model]
3-109 3qgaL 17%
[Model]

3t81: CRYSTAL STRUCTURE OF DIIRON ADENINE DEAMINASE
Solved by: X-RAY, Resolution: 2.63A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

8-406 3t81A 15%
[Model]
9-407 3t81B 16%
[Model]

3nqb: CRYSTAL STRUCTURE OF ADENINE DEAMINASE FROM AGROBACTERIUM (STR. C 58)
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

8-406 3nqbA 15%
[Model]
8-407 3nqbB 15%
[Model]

3t8l: CRYSTAL STRUCTURE OF ADENINE DEAMINASE WITH MN/FE
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

8-406 3t8lA 15%
[Model]
8-407 3t8lB 15%
[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.




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