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 ]

Model 3D Structure
Model information:
Modelled residue range: 129 to 204
Based on template: [ 1emo ]  
Sequence Identity [%]: 40%
Model date: 2015-11-06
Revision date: 2015-10-15

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 ]

This model has not been updated since 2015-10-15. In the meantime, new template structures may have become available which would allow building a more reliable model. Please use the SWISS-MODEL server to interactively compute a new model for your target protein: Build New Model Interactively



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 Nov  6 21:21:13
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 B found
 - No template with B found
 - 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 B 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
 - No template with A found
 - No template with B found
 - No template with B found
 - 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 B found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:13): model based on new templates
 - Send 13 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 4xbmB (10-200) was successful 
 -             ****************
 - building model based on 1uzjB (131-305) was successful 
 -                     **************
 - building model based on 3p5cL (218-367) was successful 
 -     ***********************
 - building model based on 4xbmB (47-296) 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 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 Nov  6 21:26:48
2015 




Template Description
Match Chain SeqId

4bv0: HIGH RESOLUTION STRUCTURE OF EVOLVED AGONIST-BOUND NEUROTENSIN RECEPTOR 1 MUTANT WITHOUT LYSOZYME FUSION
Solved by: X-RAY, Resolution: 3.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-861 4bv0A 10%
[Model]
602-862 4bv0B 10%
[Model]
764-776 4bv0B 23%
[Model]

4zwj: CRYSTAL STRUCTURE OF RHODOPSIN BOUND TO ARRESTIN BY FEMTOSLASER
Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

602-865 4zwjD 11%
[Model]
602-865 4zwjA 11%
[Model]
602-866 4zwjC 11%
[Model]
602-866 4zwjB 11%
[Model]
750-772 4zwjB 17%
[Model]

2j4y: CRYSTAL STRUCTURE OF A RHODOPSIN STABILIZING MUTANT EXPRESSED IN MAMMALIAN CELLS
Solved by: X-RAY, Resolution: 3.4A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 2j4yA 12%
[Model]
601-863 2j4yB 12%
[Model]

1f88: CRYSTAL STRUCTURE OF BOVINE RHODOPSIN
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

602-868 1f88A 12%
[Model]
601-863 1f88B 12%
[Model]

3zev: STRUCTURE OF THERMOSTABLE AGONIST-BOUND NEUROTENSIN RECEPTOR 1 MUTANT WITHOUT LYSOZYME FUSION
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

609-861 3zevB 11%
[Model]
600-861 3zevA 11%
[Model]

3c9m: STRUCTURE OF A MUTANT BOVINE RHODOPSIN IN HEXAGONAL CRYSTAFORM
Solved by: X-RAY, Resolution: 3.40A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 3c9mA 11%
[Model]

1gzm: STRUCTURE OF BOVINE RHODOPSIN IN A TRIGONAL CRYSTAL FORM
Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

600-865 1gzmA 11%
[Model]
600-865 1gzmB 11%
[Model]

2i36: CRYSTAL STRUCTURE OF TRIGONAL CRYSTAL FORM OF GROUND-STATERHODOPSIN
Solved by: X-RAY, Resolution: 4.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 2i36A 11%
[Model]
602-861 2i36B 11%
[Model]
601-860 2i36C 11%
[Model]

3cap: CRYSTAL STRUCTURE OF NATIVE OPSIN: THE G PROTEIN-COUPLED RECEPTOR RHODOPSIN IN ITS LIGAND-FREE STATE
Solved by: X-RAY, Resolution: 4.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 3capB 11%
[Model]
601-863 3capA 11%
[Model]

4pxf: CRYSTAL STRUCTURE OF THE ACTIVE G-PROTEIN-COUPLED RECEPTORCOMPLEX WITH THE FINGER-LOOP PEPTIDE DERIVED FROM THE FULARRESTIN-1
Solved by: X-RAY, Resolution: 2.75A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 4pxfA 11%
[Model]

3c9l: STRUCTURE OF GROUND-STATE BOVINE RHODOSPIN IN A HEXAGONAL CRYSTAL FORM
Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

600-865 3c9lA 11%
[Model]

4j4q: CRYSTAL STRUCTURE OF ACTIVE CONFORMATION OF GPCR OPSIN STAOCTYLGLUCOSIDE
Solved by: X-RAY, Resolution: 4.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 4j4qA 11%
[Model]

4bez: NIGHT BLINDNESS CAUSING G90D RHODOPSIN IN THE ACTIVE CONFO
Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

602-863 4bezA 11%
[Model]

4a4m: CRYSTAL STRUCTURE OF THE LIGHT-ACTIVATED CONSTITUTIVELY ACN2C,M257Y,D282C RHODOPSIN MUTANT IN COMPLEX WITH A PEPTIDRESEMBLING THE C-TERMINUS OF THE GALPHA-PROTEIN SUBUNIT (
Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 4a4mA 11%
[Model]

2x72: CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,N2C, RHODOPSIN MUTANT WITH BOUND GALPHACT PEPTIDE.
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 2x72A 11%
[Model]

1l9h: CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2.6 ANGSTROMS RESOLUTION
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-869 1l9hA 12%
[Model]
601-863 1l9hB 11%
[Model]

1hzx: CRYSTAL STRUCTURE OF BOVINE RHODOPSIN
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-869 1hzxA 12%
[Model]
601-863 1hzxB 11%
[Model]

2i35: CRYSTAL STRUCTURE OF RHOMBOHEDRAL CRYSTAL FORM OF GROUND- STATE RHODOPSIN
Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

600-865 2i35A 11%
[Model]

3pxo: CRYSTAL STRUCTURE OF METARHODOPSIN II
Solved by: X-RAY, Resolution: 4.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 3pxoA 11%
[Model]

2i37: CRYSTAL STRUCTURE OF A PHOTOACTIVATED RHODOPSIN
Solved by: X-RAY, Resolution: 4.15A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

602-865 2i37A 11%
[Model]
601-865 2i37B 11%
[Model]
601-869 2i37C 11%
[Model]

3pqr: CRYSTAL STRUCTURE OF METARHODOPSIN II IN COMPLEX WITH A C-PEPTIDE DERIVED FROM THE GALPHA SUBUNIT OF TRANSDUCIN
Solved by: X-RAY, Resolution: 4.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 3pqrA 11%
[Model]

4bey: NIGHT BLINDNESS CAUSING G90D RHODOPSIN IN COMPLEX WITH GACT2 PEPTIDE
Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

602-863 4beyA 11%
[Model]

3dqb: CRYSTAL STRUCTURE OF THE ACTIVE G-PROTEIN-COUPLED RECEPTOROPSIN IN COMPLEX WITH A C-TERMINAL PEPTIDE DERIVED FROM THE GALPHA SUBUNIT OF TRANSDUCIN
Solved by: X-RAY, Resolution: 4.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-863 3dqbA 11%
[Model]

4buo: HIGH RESOLUTION STRUCTURE OF THERMOSTABLE AGONIST-BOUND NEUROTENSIN RECEPTOR 1 MUTANT WITHOUT LYSOZYME FUSION
Solved by: X-RAY, Resolution: 2.75A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

605-861 4buoB 11%
[Model]
600-859 4buoA 11%
[Model]

2g87: CRYSTALLOGRAPHIC MODEL OF BATHORHODOPSIN
Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

598-655 2g87A 10%
[Model]
598-655 2g87B 10%
[Model]
602-883 2g87A 11%
[Model]
602-883 2g87B 11%
[Model]
827-878 2g87A 8%
[Model]
827-878 2g87B 8%
[Model]

2ped: CRYSTALLOGRAPHIC MODEL OF 9-CIS-RHODOPSIN
Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

598-655 2pedA 10%
[Model]
598-655 2pedB 10%
[Model]
602-883 2pedA 11%
[Model]
602-883 2pedB 11%
[Model]
827-878 2pedA 8%
[Model]
827-878 2pedB 8%
[Model]

5c1m: CRYSTAL STRUCTURE OF ACTIVE MU-OPIOID RECEPTOR BOUND TO THBU72
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-855 5c1mA 10%
[Model]

4bwb: STRUCTURE OF EVOLVED AGONIST-BOUND NEUROTENSIN RECEPTOR 1 MUTANT WITHOUT LYSOZYME FUSION
Solved by: X-RAY, Resolution: 3.57A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

601-861 4bwbA 12%
[Model]
602-859 4bwbB 10%
[Model]

4xes: STRUCTURE OF ACTIVE-LIKE NEUROTENSIN RECEPTOR
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

599-857 4xesA 10%
[Model]

1u19: CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2.2 ANGSTROMS RESOLUTION
Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

598-655 1u19B 10%
[Model]
598-655 1u19A 10%
[Model]
602-883 1u19B 11%
[Model]
602-883 1u19A 11%
[Model]
827-878 1u19B 8%
[Model]
827-878 1u19A 8%
[Model]

3oax: CRYSTAL STRUCTURE OF BOVINE RHODOPSIN WITH BETA-IONONE
Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

598-655 3oaxA 10%
[Model]
602-883 3oaxA 11%
[Model]
827-878 3oaxA 8%
[Model]
598-655 3oaxB 10%
[Model]
602-883 3oaxB 11%
[Model]
827-878 3oaxB 8%
[Model]

2hpy: CRYSTALLOGRAPHIC MODEL OF LUMIRHODOPSIN
Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

598-655 2hpyB 10%
[Model]
598-655 2hpyA 10%
[Model]
602-883 2hpyB 11%
[Model]
602-883 2hpyA 11%
[Model]
827-878 2hpyB 8%
[Model]
827-878 2hpyA 8%
[Model]

4xee: STRUCTURE OF ACTIVE-LIKE NEUROTENSIN RECEPTOR
Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

600-859 4xeeA 9%
[Model]

1jfp: STRUCTURE OF BOVINE RHODOPSIN (DARK ADAPTED)
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

608-869 1jfpA 11%
[Model]
822-872 1jfpA 6%
[Model]

1ln6: STRUCTURE OF BOVINE RHODOPSIN (METARHODOPSIN II)
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

608-869 1ln6A 11%
[Model]
822-872 1ln6A 6%
[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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