SWISS-MODEL Repository - Model Details

Model Overview
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1
358

Sequence
UniProt A2AS89 Agmatinase, mitochondrial (Agmatine ureohydrolase)
Mus musculus (Mouse).
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
A2AS89: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
Arginase

Model 3D Structure
Model information:
Modelled residue range: 61 to 355
Based on template: [ 3nio ]  
Sequence Identity [%]: 60%
Model date: 2014-04-11
Revision date: 2014-04-08

Quaternary structure information: [details]
Template (3nio): HEXAMER
Model: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ALA: 7, LYS: 1, MN: 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                       GVC SMMRLPLQSS ---PEGLDAA FIGVPLDTGT
3nioD     4     nlhqplggne mprfg--gia tmmrlphvqs paeldaldaa fvgvpldigt
                                                                      
TARGET                                                  sss ssss      
3nioD                                            hhhhh  sss ssss      


TARGET    31    SNRPGARFGP CRIREESLML GAVNPSTGAL PFQSLRVADL GNVNVNLYNL
3nioD     52    slrsgtrfgp reiraesvmi rpynmatgaa pfdslnvadi gdvaintfnl
                                                                      
TARGET                   h hhhhh                                     h
3nioD                    h hhhhh                  hhh                h


TARGET    81    QDSCLLIREA YQNVLAAGCI PLTLGGDQTI TYPILQAVAK EHGPVGLVHV
3nioD     102   leavriieqe ydrilghgil pltlggdhti tlpilrai-- khg-vglvhv
                                                                      
TARGET          hhhhhhhhhh hhhhhh   s sssss   hh hhhhhhh         sssss
3nioD           hhhhhhhhhh hhhhhh   s sssss   hh hhhhhhh         sssss


TARGET    131   GAHTNTTDKP REEKVYHRTP FRRSVDEGLL DSKRVVQIGI RGSSRTLDPY
3nioD     152   dahadvndhm fge-iahgtt frraveedll dcdrvvqigl raqgytaedf
                                                                      
TARGET          s                     hhhhhhh       ssssss         hhh
3nioD           s                   h hhhhhh        ssssss         hhh


TARGET    181   RYSRSQGFRV VLAEDCWMKS LVPLMAEVRQ QMGGKPLYIS FAIDALDPAY
3nioD     202   nwsr-qgfrv vqaeecw-hs leplmaevre -vgggpvyls fdidgidpaw
                                                                      
TARGET          hhhhhh  ss s  hhhh      hhhhhhhh      sssss sss       
3nioD           hh      ss s  hhh      hhhhhhh        sssss sss       


TARGET    231   APGTGTPEIA GLTPSQALEI IRGCQGLNVV GCDLVEVSPP YDLSGNTALL
3nioD     252   apgtgtpeig glttiqamei irgcqgldli gcdlvevspp ydttgntsll
                                                                      
TARGET                        hhhhhhh hhh        sssss           hhhhh
3nioD                         hhhhhhh hhh        sssss           hhhhh


TARGET    281   AANLLFEMLC ALPKV --                                   
3nioD     302   ganllyemlc vlpgvvrr                                   
                                                                      
TARGET          hhhhhhhhhh                                            
3nioD           hhhhhhhhhh                                            



Quality


Template's ligands section
Ligands in the template: ALA: 7, LYS: 1, MN: 2.
Ligands in the template that will be assessed: MN1607, MN1608.
Model's ligands section
MN1607
One or more ligand's atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other ligands.
Given the properties calculated previously, the ligand D.MN1607 will not be included in the final model.
MN1607: conservation:False, RMSD:False, included: False

MN1608
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand D.MN1608 will not be included in the final model.
MN1608: conservation:False, RMSD:False, included: False

No ligands were included in the model.


Quaternary Structure Annotation of the Template
3nio is annotated as HEXAMER
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: 3nio.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 (=HEXAMER)
The corresponding reliability score is 0.726 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 3nioC 3nioF 3nioB 3nioE 3nioA
Unfortunately, we were not able to built the model as HEXAMER.
Thus, the model was built as single chain.


Template Selection
 - Start SMR-Pipeline for:33d3b88821ac401bea467807b54d1adf on BC2-cluster at Fri Apr 11 04:41:43
2014 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange - make sure all DBs are sync'ed correctly
 - 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

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -               ******************************************************************
 - Oligomeric modeling of 3nioD was not successful, fall back to monomeric modeling
 - building model based on 3nioD (61-355) 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:33d3b88821ac401bea467807b54d1adf on BC2-cluster at Fri Apr 11 05:15:00
2014 




Template Description
Match Chain SeqId

3nio: CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA GUANIDINOBUTYR
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

61-355 3nioC 60%
[Model]
61-355 3nioF 60%
[Model]
61-355 3nioB 60%
[Model]
61-355 3nioE 60%
[Model]
61-355 3nioA 60%
[Model]
61-355 3nioD 60%
[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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