SWISS-MODEL Repository - Model Details

Model Overview
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Sequence
UniProt Q14246
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q14246: 9606.ENSP0000031

Domain
Link to: [ InterPro ]
7tm_2
GPS
EGF_CA
EGF_CA
EGF_CA
EGF_CA
cEGF

Model 3D Structure
Model information:
Modelled residue range: 129 to 204
Based on template: [ 1emo ]  
Sequence Identity [%]: 40%
Model date: 2015-04-10
Revision date: 2015-03-23

Quaternary structure information: [details]
Template (1emo): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: CA: 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       SCTDINEC LTSSVCPEHS DCVNSMGSYS CSCQVGFISR NSTCEDVDEC
1emoA     2124    savdmdec kepdvc-khg qcintdgsyr cecpfgyila gnecvdtdec
                                                                      
TARGET                                sssss  sss ss   sssss   sssss   
1emoA                                 sssss  sss ss   sssss   sssss  h


TARGET    49    ADPRACPEHA TCNNTVGNYS CFCNPGFE - ------               
1emoA     2171  svgnpc-gng tcknviggfe ctceegfepg pmmtce               
                                                                      
TARGET                     sss      s ss                              
1emoA           h          sss      s ss                              



Quality


Template's ligands section
Ligands in the template: CA: 2.
Ligands in the template that will be assessed: CA2224, CA2225.
Model's ligands section
CA2224
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 A.CA2224 will not be included in the final model.
CA2224: conservation:False, RMSD:False, included: False

CA2225
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 A.CA2225 will not be included in the final model.
CA2225: conservation:False, RMSD:False, included: False

No ligands were included in the model.


Quaternary Structure Annotation of the Template
1emo is annotated as MONOMER
The template structure (1emo) 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
The target and template sequences are too diverse (seqid: 40.789) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode

The target structure was calculated as SINGLE CHAIN


Template Selection
 - Start SMR-Pipeline for:9d934ea451abb9b6e287cef6798400f7 on BC2-cluster at Fri Apr 10 18:01:33
2015 


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

 - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - No template with B found
 - No template with P found
 - No template with A found
 - No template with P found
 - No template with A found
 - No template with P found
 - No template with A found
 - No template with P found
 - No template with A found
 - No template with P found
 - No template with A found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:12): model based on new templates
 - Send 12 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -             *******
 - building model based on 1emnA (129-204) was not successful go to next best template
 -             *******
 - building model based on 1emoA (129-204) was successful 
 -         ***********
 - building model based on 2bouA (91-208) was successful 
 -                 ***********
 - building model based on 2bouA (180-302) was successful 
 -              ***********
 - building model based on 2bo2B (142-258) was successful 
 -    ******
 - building model based on 2boxA (38-108) was successful 
 -     ***********
 - building model based on 2boxA (41-159) was successful 
 -             ****************
 - building model based on 1uzjB (131-305) was successful 
 -                     **************
 - building model based on 3p5cL (218-367) was successful 
 -                                                             *****************
 - building model based on 4l6rA (664-854) was not successful go to next best template
 -                                                        **********************
 - building model based on 4k5yC (604-848) was successful 
 -        ***************
 - building model based on 1n7dA (83-250) was successful 
 -                                    ******************
 - building model based on 4dlqA (387-584) was not successful go to next best template
 - 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:9d934ea451abb9b6e287cef6798400f7 on BC2-cluster at Fri Apr 10 18:04:34
2015 




Template Description
Match Chain SeqId

1n1i: THE STRUCTURE OF MSP-1(19) FROM PLASMODIUM KNOWLESI
Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

134-207 1n1iA 17%
[Model]
174-305 1n1iA 13%
[Model]
31-115 1n1iA 19%
[Model]
89-171 1n1iA 14%
[Model]
134-207 1n1iB 17%
[Model]
174-207 1n1iB 26%
[Model]
31-115 1n1iB 19%
[Model]
90-171 1n1iB 15%
[Model]
135-207 1n1iC 18%
[Model]
175-207 1n1iC 29%
[Model]
32-115 1n1iC 19%
[Model]
90-171 1n1iC 16%
[Model]
134-207 1n1iD 17%
[Model]
174-304 1n1iD 13%
[Model]
31-115 1n1iD 19%
[Model]
40-65 1n1iD 23%
[Model]
90-170 1n1iD 15%
[Model]

1b9w: C-TERMINAL MEROZOITE SURFACE PROTEIN 1 FROM PLASMODIUM CYNOMOLGI
Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

140-202 1b9wA 21%
[Model]
32-114 1b9wA 20%
[Model]
90-170 1b9wA 17%
[Model]

2npr: STRUCTURAL STUDIES ON PLASMODIUM VIVAX MEROZOITE SURFACE PROTEIN-1
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

140-207 2nprA 19%
[Model]
174-302 2nprA 11%
[Model]
32-117 2nprA 21%
[Model]
90-165 2nprA 15%
[Model]

4u16: M3-MT4L RECEPTOR BOUND TO NMS
Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

603-859 4u16B 7%
[Model]
602-773 4u16A 9%
[Model]

4u15: M3-MT4L RECEPTOR BOUND TO TIOTROPIUM
Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

602-858 4u15A 7%
[Model]
603-859 4u15B 7%
[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.