SWISS-MODEL Repository - Model Details

Model Overview
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1
140

Sequence
UniProt P12025
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P12025: 10090.ENSMUSP000

Domain
Link to: [ InterPro ]
PTN_MK_C
PTN_MK_N

Model 3D Structure
Model information:
Modelled residue range: 31 to 78
Based on template: [ 1mkn ]  
Sequence Identity [%]: 87%
Model date: 2013-05-08
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (1mkn): MONOMER
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 ]

Alignment 

TARGET    1                   GSECSEW TWGPCTPSSK DCGMGFREGT CGAQTQRVHC
1mknA     1     kkkdkvkkgg p--gsecaew awgpctpssk dcgvgfregt cgaqtqrirc
                                                                      
TARGET                                sss            ssssss      sssss
1mknA                                 sss            ssssss      sssss


TARGET    38    KVPCNWKKEF G                                          
1mknA     49    rvpcnwkkef g-                                         
                                                                      
TARGET                                                                
1mknA

Quality 


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

 
Quaternary Structure Annotation of the Template 
 1mkn is annotated as MONOMER 
 The template structure (1mkn) was solved by NMR and does not contain any quaternary structure annotation 
 The template is annotated by the number of chains found in the PDB file 
      
 
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 0.256 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:3473e3dbf4db43143aa260ff8efd7729 on BC2-cluster at Wed May  8 04:18:47
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  2 go for
modeling ...

 - No A3m 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 1mkcA (81-123) was not successful go to next best template
 -                   ***************************
 - building model based on 1mknA (31-78) 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:3473e3dbf4db43143aa260ff8efd7729 on BC2-cluster at Wed May  8 04:19:58
2013


Template Description
Match Chain SeqId

1mkc: C-TERMINAL DOMAIN OF MIDKINE
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

81-123 1mkcA 93%
[Model]

1mkn: N-TERMINAL HALF OF MIDKINE
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

31-78 1mknA 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.