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Model Overview
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1
378

Sequence
UniProt P47774
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]

Model 3D Structure
Model information:
Modelled residue range: 54 to 250
Based on template: [ 3oe9 ]  
Sequence Identity [%]: 40%
Model date: 2015-11-01
Revision date: 2015-10-15

Quaternary structure information: [details]
Template (3oe9): DIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ITD: 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 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         RNFKAW FLPLMYSVIC FVGLLGNGLV ILTYIYFKRL KTMTDTYLLN
3oe9A     28    cf--rnfnki flptiysiif ltgivgnglv ilvmgyqkkl rsmtdkyrlh
                                                                      
TARGET                        hhhhhhh hhhhhhhhhh hhhh          hhhhhhh
3oe9A                       hhhhhhhhh hhhhhhhhhh hhhhh         hhhhhhh


TARGET    47    LAVADILFLL ILPFWAYSEA KSWIFGVYLC KGIFGIYKLS FFSGMLLLLC
3oe9A     80    lsvadllfvi tlpfwavdav anwyfgnflc kavhviytvn lyssvwilaf
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh       hhhh hhhhhhhhhh hhhhhhhhhh
3oe9A           hhhhhhhhhh hhhhhhhhhh       hhhh hhhhhhhhhh hhhhhhhhhh


TARGET    97    ISIDRYVAIV QAVSAHRHRA RVLLISKLSC VGIWMLALFL SIPELLYSGL
3oe9A     130   isldrylaiv hatnsqrprk --llaekvvy vgvwipalll tipdfifanv
                                                                      
TARGET          hhhhhhhhhh                    h    hhhhhhhh hhhh  ssss
3oe9A           hhhhhhhhh          hh   hhh   h    hhhhhh    hhh  ssss


TARGET    147   QKNSGEDTLR CSLVSAQVEA LITIQVAQMV FGFLVPMLAM SFCYLIIIRT
3oe9A     178   se--addryi cdrfypndlw vvvfqfqhim vglilpgivi lscyciiisk
                                                                      
TARGET          s        s ssss    hh hhh   hhhh h   hhhhhh hhhhhhhhhh
3oe9A           s        s ssss    hh hhh   hhhh h   hhhhhh hhhhhhhhhh


TARGET    197   L -------- ---------- ---------- ---------- ----------
3oe9A     226   lshnifemlr ideglrlkiy kgyytigigh lltkspslna akseldkaig
                                                                      
TARGET                                                                
3oe9A              hhhhhhh hhh   sss     sss   s ss     hhh hhhhhh    


TARGET          ---------- ---------- ---------- ---------- ----------
3oe9A     1052  rntngvitkd eaeklfnqdv daavrgilrn aklkpvydsl davrraalin
                                                                      
TARGET                                                                
3oe9A               sss hh hhhhhhhhhh hhhhhh   h hhhhhhhh    hhhhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
3oe9A     1102  mvfqmgetgv agftnslrml qqkrwdeaav nlaksrwynq tpnrakrvit
                                                                      
TARGET                                                                
3oe9A           hhh   hhhh h   hhhhhh    hhhhhhh hh    h    hhhhhhhhhh


TARGET          ---------- ---------- ---------- ---------- ----------
3oe9A     1152  tfrtgtwday kalkptvili laffacwlpy yigisidsfi lleiikcefe
                                                                      
TARGET                                                                
3oe9A           hhhh          hhhhhhh hhhhhhhhhh hhhhhhhhhh h      hhh


TARGET          ---------- ---------- ------                          
3oe9A     278   ntvhkwisit ealaffhccl npilya                          
                                                                      
TARGET                                                                
3oe9A           hhhhhhhhhh hhhhhhh    hhh                             



Quality


Template's ligands section
Ligands in the template: ITD: 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
3oe9 is annotated as DIMER
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: 3oe9.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 (=DIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.006 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 3oe9B


Template Selection
 - Start SMR-Pipeline for:c45dd7e71693b788cb938da5aabe8195 on BC2-cluster at Sun Nov  1 12:24:43
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 B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with I found
 - No template with I found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with G found
 - No template with N found
 - No template with B found
 - No template with B found
 - No template with B 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 3oe9A (54-250) was successful 
 -            *************************************************************
 - building model based on 2lnlA (52-341) 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:c45dd7e71693b788cb938da5aabe8195 on BC2-cluster at Sun Nov  1 12:31:58
2015 




Template Description
Match Chain SeqId

1fdf: HELIX 7 BOVINE RHODOPSIN
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

314-335 1fdfA 27%
[Model]

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 ]  

56-344 4bv0A 25%
[Model]
55-345 4bv0B 25%
[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 ]  

56-345 4bwbA 25%
[Model]
56-341 4bwbB 25%
[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 ]  

57-337 5c1mA 25%
[Model]

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

56-350 4xeeA 24%
[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 ]  

55-341 4buoA 25%
[Model]
55-343 4buoB 24%
[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 ]  

55-343 3zevB 24%
[Model]
55-343 3zevA 25%
[Model]

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

56-342 4xesA 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 ]  

59-343 4zwjC 19%
[Model]
59-343 4zwjD 19%
[Model]
59-343 4zwjA 19%
[Model]
57-343 4zwjB 20%
[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 ]  

55-343 2i35A 19%
[Model]

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

63-343 1ln6A 19%
[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 ]  

55-343 1gzmA 19%
[Model]
55-343 1gzmB 19%
[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 ]  

55-343 3c9lA 19%
[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 ]  

57-343 3c9mA 19%
[Model]

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

63-343 1jfpA 19%
[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 ]  

57-343 2x72A 19%
[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 ]  

55-343 4a4mA 19%
[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 ]  

56-343 4beyA 18%
[Model]

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

56-343 3pxoA 18%
[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 ]  

56-343 3oaxA 18%
[Model]
56-343 3oaxB 18%
[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 ]  

56-343 4j4qA 18%
[Model]

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

55-342 1f88A 19%
[Model]
57-343 1f88B 18%
[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 ]  

56-343 3pqrA 18%
[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 ]  

55-343 1l9hA 19%
[Model]
57-343 1l9hB 18%
[Model]

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

58-337 2i37A 19%
[Model]
56-343 2i37B 18%
[Model]
56-352 2i37C 18%
[Model]

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

56-343 2g87A 18%
[Model]
56-343 2g87B 18%
[Model]

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

56-343 2pedA 18%
[Model]
56-343 2pedB 18%
[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 ]  

56-343 1u19B 18%
[Model]
56-343 1u19A 18%
[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 ]  

56-343 4bezA 18%
[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 ]  

55-343 2j4yA 18%
[Model]
55-343 2j4yB 18%
[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 ]  

56-343 2i36A 18%
[Model]
57-342 2i36B 18%
[Model]
56-341 2i36C 19%
[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 ]  

56-343 3capB 18%
[Model]
56-343 3capA 18%
[Model]

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

56-343 2hpyB 18%
[Model]
56-343 2hpyA 18%
[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 ]  

56-343 3dqbA 18%
[Model]

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

55-343 1hzxA 19%
[Model]
57-343 1hzxB 18%
[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 ]  

56-343 4pxfA 18%
[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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