SWISS-MODEL Repository - Model Details

Model Overview
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Sequence
UniProt P56475
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]

Model 3D Structure
Model information:
Modelled residue range: 311 to 370
Based on template: [ 1vry ]  
Sequence Identity [%]: 60%
Model date: 2015-11-05
Revision date: 2015-10-15

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

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 ]

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       VPARVPLG ITTVLTMSTI ITGVNASMPR VSYIKAVDIY LWVSFVFVFL
1vry_1#3  65533    lparvglg ittvltlttq ssgsraslpk vsyvkaidiw lavcllfvfs
                                                                      
TARGET              hhhhhh hhhhhhhhhh hh         hhhhhh   h hhhhhhhhhh
1vry_1#3            hhhhhh hhhhhhhhhh hh         hhhhhh   h hhhhhhhhhh


TARGET    49    SVLEYAAVNY LT                                         
1vry_1#3  45    alleyaavnf vsr                                        
                                                                      
TARGET          hhhhhhhhhh h                                          
1vry_1#3        hhhhhhhhhh h                                          



Quality


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


Quaternary Structure Annotation of the Template
1vry is annotated as MONOMER
The template structure (1vry) 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: 60.000) 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
Model was succesfully built as MONOMER.


Template Selection
 - Start SMR-Pipeline for:c35168c19a39d8ed32602dc78a7a3765 on BC2-cluster at Thu Nov  5 11:10:42
2015 


 - 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...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - Skipping oligomeric state prediction due to too many templates for cluster: 96_369
 - Skip Template HHsearch issue
 - Warning: Oligomer Prediction was not successfull!

 - Warning: clustersMergedFile not found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:5): model based on new templates
 - Send 5 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                     **********
 - building model based on 1vryA (311-370) was successful 
 -                                               ****************
 - building model based on 2m6bA (278-374) was successful 
 -               ************************************************
 - building model based on 4cofA (85-369) was successful 
 -                                               **********************************
 - building model based on 2m6bA (277-479) was successful 
 -              *******************************************************************
 - building model based on 5cfbA (76-479) 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:c35168c19a39d8ed32602dc78a7a3765 on BC2-cluster at Thu Nov  5 11:13:07
2015 




Template Description
Match Chain SeqId

1vry: SECOND AND THIRD TRANSMEMBRANE DOMAINS OF THE ALPHA-1 SUBUNIT OF HUMAN GLYCINE RECEPTOR
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

311-370 1vryA 60%
[Model]
311-371 1vryA 59%
[Model]

2m6i: PUTATIVE PENTAMERIC OPEN-CHANNEL STRUCTURE OF FULL-LENGTH TRANSMEMBRANE DOMAINS OF HUMAN GLYCINE RECEPTOR ALPHA1 SU
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

277-479 2m6iD 33%
[Model]
277-479 2m6iC 33%
[Model]
277-479 2m6iB 33%
[Model]
277-479 2m6iE 33%
[Model]
277-479 2m6iA 33%
[Model]

5cfb: CRYSTAL STRUCTURE OF HUMAN GLYCINE RECEPTOR ALPHA-3 BOUND STRYCHNINE
Solved by: X-RAY, Resolution: 3.04A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

76-479 5cfbA 33%
[Model]
76-479 5cfbB 33%
[Model]
76-479 5cfbE 33%
[Model]
74-479 5cfbC 32%
[Model]
74-479 5cfbD 33%
[Model]

2m6b: STRUCTURE OF FULL-LENGTH TRANSMEMBRANE DOMAINS OF HUMAN GLRECEPTOR ALPHA1 MONOMER SUBUNIT
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

277-479 2m6bA 33%
[Model]

3jad: STRUCTURE OF ALPHA-1 GLYCINE RECEPTOR BY SINGLE PARTICLE ECRYO-MICROSCOPY, STRYCHNINE-BOUND STATE
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

73-479 3jadB 32%
[Model]
73-479 3jadE 32%
[Model]
73-479 3jadA 32%
[Model]
73-479 3jadD 32%
[Model]
73-479 3jadC 32%
[Model]

3jae: STRUCTURE OF ALPHA-1 GLYCINE RECEPTOR BY SINGLE PARTICLE ECRYO-MICROSCOPY, GLYCINE-BOUND STATE
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

76-479 3jaeA 32%
[Model]
76-479 3jaeD 32%
[Model]
76-479 3jaeC 32%
[Model]
76-479 3jaeB 32%
[Model]
76-479 3jaeE 32%
[Model]

3jaf: STRUCTURE OF ALPHA-1 GLYCINE RECEPTOR BY SINGLE PARTICLE ECRYO-MICROSCOPY, GLYCINE/IVERMECTIN-BOUND STATE
Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

75-479 3jafC 32%
[Model]
75-479 3jafB 32%
[Model]
75-479 3jafE 32%
[Model]
75-479 3jafA 32%
[Model]
75-479 3jafD 32%
[Model]

2yks: PENTAMERIC LIGAND GATED ION CHANNEL ELIC MUTANT F246A
Solved by: X-RAY, Resolution: 3.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 2yksC 18%
[Model]
97-370 2yksJ 18%
[Model]
97-370 2yksF 18%
[Model]
97-370 2yksB 18%
[Model]
97-370 2yksI 18%
[Model]
97-370 2yksE 18%
[Model]
97-370 2yksA 18%
[Model]
97-370 2yksH 18%
[Model]
97-370 2yksD 18%
[Model]
97-370 2yksG 18%
[Model]

4twh: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) MUTANT F16'S
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 4twhI 18%
[Model]
97-370 4twhE 18%
[Model]
97-370 4twhA 18%
[Model]
97-370 4twhH 18%
[Model]
97-370 4twhD 18%
[Model]
97-370 4twhG 18%
[Model]
97-370 4twhC 18%
[Model]
97-370 4twhJ 18%
[Model]
97-370 4twhF 18%
[Model]
97-370 4twhB 18%
[Model]

4twd: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) IN COMPLEX WITH MEMANTINE
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 4twdG 18%
[Model]
97-370 4twdC 18%
[Model]
97-370 4twdJ 18%
[Model]
97-370 4twdF 18%
[Model]
97-370 4twdB 18%
[Model]
97-370 4twdI 18%
[Model]
97-370 4twdE 18%
[Model]
97-370 4twdA 18%
[Model]
97-370 4twdH 18%
[Model]
97-370 4twdD 18%
[Model]

4z90: ELIC BOUND WITH THE ANESTHETIC ISOFLURANE IN THE RESTING S
Solved by: X-RAY, Resolution: 3.39A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

96-369 4z90I 18%
[Model]
96-369 4z90E 18%
[Model]
96-369 4z90A 18%
[Model]
96-369 4z90H 18%
[Model]
96-369 4z90D 18%
[Model]
96-369 4z90G 18%
[Model]
96-369 4z90C 18%
[Model]
96-369 4z90J 18%
[Model]
96-369 4z90F 18%
[Model]
96-369 4z90B 18%
[Model]

2yoe: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) IN COMPLEX WITH GABA ANDFLURAZEPAM
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 2yoeD 18%
[Model]
97-370 2yoeG 18%
[Model]
97-370 2yoeC 18%
[Model]
97-370 2yoeJ 18%
[Model]
97-370 2yoeF 18%
[Model]
97-370 2yoeB 18%
[Model]
97-370 2yoeI 18%
[Model]
97-370 2yoeE 18%
[Model]
97-370 2yoeA 18%
[Model]
97-370 2yoeH 18%
[Model]

3uq5: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) MUTANT L240A F247L (L9A F16L) IN THE 10 MM CYSTEAMINE
Solved by: X-RAY, Resolution: 4.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 3uq5D 18%
[Model]
97-370 3uq5G 18%
[Model]
97-370 3uq5C 18%
[Model]
97-370 3uq5J 18%
[Model]
97-370 3uq5F 18%
[Model]
97-370 3uq5B 18%
[Model]
97-370 3uq5I 18%
[Model]
97-370 3uq5E 18%
[Model]
97-370 3uq5A 18%
[Model]
97-370 3uq5H 18%
[Model]

4a97: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) IN COMPLEX WITH ZOPICLON
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 4a97F 18%
[Model]
97-370 4a97B 18%
[Model]
97-370 4a97I 18%
[Model]
97-370 4a97E 18%
[Model]
97-370 4a97A 18%
[Model]
97-370 4a97H 18%
[Model]
97-370 4a97D 18%
[Model]
97-370 4a97G 18%
[Model]
97-370 4a97C 18%
[Model]
97-370 4a97J 18%
[Model]

4twf: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) IN COMPLEX WITH BROMOMEMANTINE
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 4twfA 18%
[Model]
97-370 4twfH 18%
[Model]
97-370 4twfD 18%
[Model]
97-370 4twfG 18%
[Model]
97-370 4twfC 18%
[Model]
97-370 4twfJ 18%
[Model]
97-370 4twfF 18%
[Model]
97-370 4twfB 18%
[Model]
97-370 4twfI 18%
[Model]
97-370 4twfE 18%
[Model]

3rqw: CRYSTAL STRUCTURE OF ACETYLCHOLINE BOUND TO A PROKARYOTIC LIGAND-GATED ION CHANNEL, ELIC
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 3rqwF 18%
[Model]
97-370 3rqwB 18%
[Model]
97-370 3rqwI 18%
[Model]
97-370 3rqwE 18%
[Model]
97-370 3rqwA 18%
[Model]
97-370 3rqwH 18%
[Model]
97-370 3rqwD 18%
[Model]
97-370 3rqwG 18%
[Model]
97-370 3rqwC 18%
[Model]
97-370 3rqwJ 18%
[Model]

3zkr: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) IN COMPLEX WITH BROMOFOR
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 3zkrA 18%
[Model]
97-370 3zkrH 18%
[Model]
97-370 3zkrD 18%
[Model]
97-370 3zkrG 18%
[Model]
97-370 3zkrC 18%
[Model]
97-370 3zkrJ 18%
[Model]
97-370 3zkrF 18%
[Model]
97-370 3zkrB 18%
[Model]
97-370 3zkrI 18%
[Model]
97-370 3zkrE 18%
[Model]

3uq7: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) MUTANT L240S F247L (L9S F16L) IN PRESMM CYSTEAMINE
Solved by: X-RAY, Resolution: 3.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-369 3uq7E 18%
[Model]
97-369 3uq7A 18%
[Model]
97-369 3uq7H 18%
[Model]
97-369 3uq7D 18%
[Model]
97-369 3uq7G 18%
[Model]
97-369 3uq7C 18%
[Model]
97-369 3uq7J 18%
[Model]
97-369 3uq7F 18%
[Model]
97-369 3uq7B 18%
[Model]
97-369 3uq7I 18%
[Model]

2yn6: PENTAMERIC LIGAND-GATED ION CHANNEL ELIC IN COMPLEX WITH BARIUM
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 2yn6C 18%
[Model]
97-370 2yn6B 18%
[Model]
97-370 2yn6E 18%
[Model]
97-370 2yn6A 18%
[Model]
97-370 2yn6D 18%
[Model]

4z91: ELIC COCRYSTALLIZED WITH ISOFLUORANE IN A DESENSITIZED STA
Solved by: X-RAY, Resolution: 3.39A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

96-369 4z91D 18%
[Model]
96-369 4z91G 18%
[Model]
96-369 4z91C 18%
[Model]
96-369 4z91J 18%
[Model]
96-369 4z91F 18%
[Model]
96-369 4z91B 18%
[Model]
96-369 4z91I 18%
[Model]
96-369 4z91E 18%
[Model]
96-369 4z91A 18%
[Model]
96-369 4z91H 18%
[Model]

3rqu: CRYSTAL STRUCTURE OF A PROKARYOTIC PENTAMERIC LIGAND-GATEDCHANNEL, ELIC
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 3rquI 18%
[Model]
97-370 3rquE 18%
[Model]
97-370 3rquA 18%
[Model]
97-370 3rquH 18%
[Model]
97-370 3rquD 18%
[Model]
97-370 3rquG 18%
[Model]
97-370 3rquC 18%
[Model]
97-370 3rquJ 18%
[Model]
97-370 3rquF 18%
[Model]
97-370 3rquB 18%
[Model]

3uq4: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FCHRYSANTHEMI (ELIC) MUTANT F247L (F16L)
Solved by: X-RAY, Resolution: 3.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 3uq4I 18%
[Model]
97-370 3uq4E 18%
[Model]
97-370 3uq4A 18%
[Model]
97-370 3uq4H 18%
[Model]
97-370 3uq4D 18%
[Model]
97-370 3uq4G 18%
[Model]
97-370 3uq4C 18%
[Model]
97-370 3uq4J 18%
[Model]
97-370 3uq4F 18%
[Model]
97-370 3uq4B 18%
[Model]

4a98: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC) IN COMPLEX WITH BROMOFLURAZEPAM
Solved by: X-RAY, Resolution: 3.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-370 4a98A 18%
[Model]
97-370 4a98H 18%
[Model]
97-370 4a98D 18%
[Model]
97-370 4a98G 18%
[Model]
97-370 4a98C 18%
[Model]
97-370 4a98J 18%
[Model]
97-370 4a98F 18%
[Model]
97-370 4a98B 18%
[Model]
97-370 4a98I 18%
[Model]
97-370 4a98E 18%
[Model]

4yeu: ION CHANNEL
Solved by: X-RAY, Resolution: 4.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-479 4yeuC 16%
[Model]
97-479 4yeuB 16%
[Model]
97-479 4yeuE 16%
[Model]
97-479 4yeuA 16%
[Model]
97-479 4yeuD 16%
[Model]

2vl0: X-RAY STRUCTURE OF A PENTAMERIC LIGAND GATED ION CHANNEL FROM ERWINIA CHRYSANTHEMI (ELIC)
Solved by: X-RAY, Resolution: 3.3A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

97-476 2vl0E 14%
[Model]
97-476 2vl0A 14%
[Model]
97-476 2vl0H 14%
[Model]
97-476 2vl0D 14%
[Model]
97-476 2vl0G 14%
[Model]
97-476 2vl0C 14%
[Model]
97-476 2vl0J 14%
[Model]
97-476 2vl0F 14%
[Model]
97-476 2vl0B 14%
[Model]
97-476 2vl0I 14%
[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.