SWISS-MODEL Repository - Model Details

Model Overview
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1
480

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

Domain
Link to: [ InterPro ]
Neur_chan_LBD
Neur_chan_memb

Model 3D Structure
Model information:
Modelled residue range: 311 to 370
Based on template: [ 1vry ]  
Sequence Identity [%]: 60%
Model date: 2014-10-08
Revision date: 2014-10-06

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 ]

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 Wed Oct  8 09:53:59
2014 


 - 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: 
 - No template with A found
 - No template with B found
 - No template with E found
 - No template with C found
 - No template with D found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with K found
 - No template with L found
 - No template with N found
 - No template with O found
 - No template with J found
 - No template with M found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with f found
 - No template with g found
 - No template with h found
 - No template with i found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with K found
 - No template with L found
 - No template with N found
 - No template with O found
 - No template with J found
 - No template with I found
 - No template with M found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with f found
 - No template with g found
 - No template with h found
 - No template with i found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 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 
 - 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 Wed Oct  8 12:01:12
2014 




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 BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

311-370 1vryA 60%
[Model]

1ux2: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP)
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-281 1ux2A 17%
[Model]
78-281 1ux2D 17%
[Model]
78-281 1ux2C 17%
[Model]
78-281 1ux2B 18%
[Model]
78-281 1ux2E 18%
[Model]
78-281 1ux2H 17%
[Model]
78-281 1ux2F 17%
[Model]
78-281 1ux2I 18%
[Model]
78-281 1ux2G 18%
[Model]
78-281 1ux2J 18%
[Model]

1uw6: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) ICOMPLEX WITH NICOTINE
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-283 1uw6A 17%
[Model]
78-283 1uw6D 17%
[Model]
78-281 1uw6C 18%
[Model]
78-281 1uw6B 18%
[Model]
78-281 1uw6E 18%
[Model]
78-283 1uw6F 17%
[Model]
78-281 1uw6J 18%
[Model]
78-281 1uw6I 18%
[Model]
78-281 1uw6H 18%
[Model]
78-281 1uw6G 18%
[Model]
78-283 1uw6M 17%
[Model]
78-283 1uw6N 17%
[Model]
78-281 1uw6L 18%
[Model]
78-281 1uw6O 18%
[Model]
78-281 1uw6K 18%
[Model]
78-283 1uw6T 17%
[Model]
78-283 1uw6R 17%
[Model]
78-281 1uw6Q 18%
[Model]
78-281 1uw6P 18%
[Model]
78-281 1uw6S 18%
[Model]

1i9b: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP)
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-281 1i9bA 17%
[Model]
78-281 1i9bD 17%
[Model]
78-281 1i9bC 17%
[Model]
78-281 1i9bB 17%
[Model]
78-281 1i9bE 17%
[Model]

1uv6: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) ICOMPLEX WITH CARBAMYLCHOLINE
Solved by: X-RAY, Resolution: 4.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-281 1uv6B 17%
[Model]
78-281 1uv6E 17%
[Model]
78-281 1uv6A 17%
[Model]
78-281 1uv6D 17%
[Model]
78-281 1uv6C 17%
[Model]
78-281 1uv6I 17%
[Model]
78-281 1uv6H 17%
[Model]
78-281 1uv6G 17%
[Model]
78-281 1uv6J 17%
[Model]
78-281 1uv6F 17%
[Model]

2zjv: CRYSTAL STRUCTURE OF LYMNAEA STAGNALIS ACETYLCHOLINE BINDING PROTEIN (LS-ACHBP) COMPLEXED WITH CLOTHIANIDIN
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-283 2zjvB 17%
[Model]
77-283 2zjvC 17%
[Model]
78-283 2zjvE 17%
[Model]
78-283 2zjvA 17%
[Model]
78-283 2zjvD 17%
[Model]

2zju: CRYSTAL STRUCTURE OF LYMNAEA STAGNALIS ACETYLCHOLINE BINDING PROTEIN (LS-ACHBP) COMPLEXED WITH IMIDACLOPRID
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-283 2zjuB 17%
[Model]
78-282 2zjuA 18%
[Model]
78-283 2zjuD 17%
[Model]
78-283 2zjuC 17%
[Model]
78-283 2zjuE 17%
[Model]

3u8k: CRYSTAL STRUCTURE OF THE ACETYLCHOLINE BINDING PROTEIN (ACLYMNAEA STAGNALIS IN COMPLEX WITH NS3573 (1-(5-ETHOXYPYRI4-DIAZEPANE)
Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-285 3u8kA 17%
[Model]
78-281 3u8kB 16%
[Model]
78-281 3u8kE 16%
[Model]
78-283 3u8kD 16%
[Model]
78-281 3u8kC 17%
[Model]
78-287 3u8kH 16%
[Model]
78-282 3u8kF 16%
[Model]
77-281 3u8kJ 16%
[Model]
77-281 3u8kI 16%
[Model]
78-281 3u8kG 16%
[Model]
77-287 3u8kM 16%
[Model]
78-282 3u8kK 16%
[Model]
78-286 3u8kN 16%
[Model]
77-281 3u8kO 16%
[Model]
77-281 3u8kL 16%
[Model]
78-281 3u8kP 16%
[Model]
77-281 3u8kQ 16%
[Model]
78-281 3u8kS 17%
[Model]
78-283 3u8kT 16%
[Model]
78-281 3u8kR 16%
[Model]

4nzb: NS9283 BOUND TO LS-ACHBP
Solved by: X-RAY, Resolution: 2.68A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-281 4nzbG 16%
[Model]
77-281 4nzbJ 16%
[Model]
77-281 4nzbH 16%
[Model]
78-281 4nzbF 16%
[Model]
78-281 4nzbI 16%
[Model]
77-281 4nzbC 16%
[Model]
77-281 4nzbB 16%
[Model]
77-281 4nzbE 16%
[Model]
77-281 4nzbA 16%
[Model]
77-281 4nzbD 16%
[Model]
77-281 4nzbN 16%
[Model]
77-281 4nzbL 16%
[Model]
77-281 4nzbO 16%
[Model]
78-281 4nzbK 16%
[Model]
77-281 4nzbM 16%
[Model]

3u8m: CRYSTAL STRUCTURE OF THE ACETYLCHOLINE BINDING PROTEIN (ACLYMNAEA STAGNALIS IN COMPLEX WITH NS3920 (1-(6-BROMOPYRID4-DIAZEPANE)
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-281 3u8mD 16%
[Model]
78-282 3u8mC 16%
[Model]
77-281 3u8mB 16%
[Model]
77-282 3u8mA 16%
[Model]
78-281 3u8mE 16%
[Model]
77-283 3u8mF 16%
[Model]
77-281 3u8mG 16%
[Model]
77-283 3u8mI 16%
[Model]
78-281 3u8mJ 16%
[Model]
78-281 3u8mH 16%
[Model]
77-283 3u8mL 16%
[Model]
78-281 3u8mM 16%
[Model]
78-281 3u8mO 16%
[Model]
78-281 3u8mN 16%
[Model]
78-283 3u8mK 16%
[Model]
78-281 3u8mP 16%
[Model]
77-281 3u8mR 16%
[Model]
77-281 3u8mQ 16%
[Model]
78-281 3u8mT 16%
[Model]
78-281 3u8mS 16%
[Model]

1yi5: CRYSTAL STRUCTURE OF THE A-COBRATOXIN-ACHBP COMPLEX
Solved by: X-RAY, Resolution: 4.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-282 1yi5C 16%
[Model]
78-281 1yi5D 17%
[Model]
78-281 1yi5A 16%
[Model]
78-281 1yi5B 17%
[Model]
78-281 1yi5E 16%
[Model]

3zdg: CRYSTAL STRUCTURE OF LS-ACHBP COMPLEXED WITH CARBAMOYLCHOLANALOGUE 3-(DIMETHYLAMINO)BUTYL DIMETHYLCARBAMATE (DMABC)
Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-281 3zdgM 16%
[Model]
77-281 3zdgL 16%
[Model]
77-281 3zdgK 16%
[Model]
78-281 3zdgO 16%
[Model]
78-281 3zdgN 16%
[Model]
77-281 3zdgE 16%
[Model]
77-281 3zdgD 16%
[Model]
78-281 3zdgC 17%
[Model]
78-281 3zdgA 16%
[Model]
78-281 3zdgB 16%
[Model]
77-281 3zdgI 16%
[Model]
78-281 3zdgF 16%
[Model]
78-281 3zdgH 16%
[Model]
78-281 3zdgG 16%
[Model]
78-281 3zdgJ 16%
[Model]
77-281 3zdgP 16%
[Model]
77-281 3zdgR 16%
[Model]
77-281 3zdgS 16%
[Model]
78-281 3zdgT 16%
[Model]
78-281 3zdgQ 16%
[Model]

4alx: CRYSTAL STRUCTURE OF LS-ACHBP COMPLEXED WITH THE POTENT NAANTAGONIST DHBE
Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-281 4alxF 17%
[Model]
77-281 4alxI 16%
[Model]
78-281 4alxJ 16%
[Model]
78-281 4alxH 16%
[Model]
78-281 4alxG 16%
[Model]
78-287 4alxA 17%
[Model]
78-281 4alxD 17%
[Model]
78-281 4alxE 16%
[Model]
78-281 4alxC 16%
[Model]
78-281 4alxB 16%
[Model]

4qac: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IWITH 4-(4-METHYLPIPERIDIN-1-YL)-6-(4-(TRIFLUOROMETHYL)PHEPYRIMIDIN-2-AMINE
Solved by: X-RAY, Resolution: 2.98A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-281 4qacF 17%
[Model]
78-281 4qacB 16%
[Model]
76-281 4qacE 17%
[Model]
76-286 4qacD 16%
[Model]
78-281 4qacJ 16%
[Model]
76-281 4qacI 16%
[Model]
76-281 4qacC 16%
[Model]
76-281 4qacA 16%
[Model]
76-281 4qacG 16%
[Model]
75-281 4qacH 16%
[Model]

3zdh: CRYSTAL STRUCTURE OF LS-ACHBP COMPLEXED WITH CARBAMOYLCHOLINE ANALOGUE N,N-DIMETHYL-4-(1-METHYL-1H- IMIDAZOL-2-YLOXY)BUTAN-2-AMINE
Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-281 3zdhC 16%
[Model]
78-281 3zdhE 16%
[Model]
78-281 3zdhA 16%
[Model]
78-281 3zdhD 16%
[Model]
78-281 3zdhB 16%
[Model]
78-281 3zdhF 16%
[Model]
77-281 3zdhI 16%
[Model]
78-281 3zdhH 16%
[Model]
78-281 3zdhJ 16%
[Model]
78-281 3zdhG 16%
[Model]

3u8l: CRYSTAL STRUCTURE OF THE ACETYLCHOLINE BINDING PROTEIN (ACLYMNAEA STAGNALIS IN COMPLEX WITH NS3570 (1-(5-PHENYLPYRI4-DIAZEPANE)
Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-281 3u8lB 17%
[Model]
77-281 3u8lD 16%
[Model]
78-282 3u8lE 17%
[Model]
77-281 3u8lA 16%
[Model]
78-281 3u8lC 16%
[Model]
77-282 3u8lJ 16%
[Model]
78-281 3u8lI 17%
[Model]
78-281 3u8lH 16%
[Model]
77-281 3u8lF 16%
[Model]
78-281 3u8lG 16%
[Model]

3u8j: CRYSTAL STRUCTURE OF THE ACETYLCHOLINE BINDING PROTEIN (ACLYMNAEA STAGNALIS IN COMPLEX WITH NS3531 (1-(PYRIDIN-3-YLDIAZEPANE)
Solved by: X-RAY, Resolution: 2.68A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-287 3u8jB 17%
[Model]
78-282 3u8jA 17%
[Model]
78-281 3u8jD 17%
[Model]
78-281 3u8jC 17%
[Model]
77-281 3u8jE 16%
[Model]
77-281 3u8jG 17%
[Model]
77-281 3u8jJ 16%
[Model]
78-281 3u8jI 16%
[Model]
77-281 3u8jF 16%
[Model]
78-281 3u8jH 16%
[Model]

3wip: CRYSTAL STRUCTURE OF ACETYLCHOLINE BOUND TO LS-ACHBP
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-281 3wipD 16%
[Model]
78-281 3wipE 16%
[Model]
78-281 3wipA 16%
[Model]
78-287 3wipB 16%
[Model]
78-281 3wipC 16%
[Model]
77-281 3wipG 16%
[Model]
77-281 3wipH 16%
[Model]
77-281 3wipJ 16%
[Model]
78-281 3wipI 16%
[Model]
77-286 3wipF 16%
[Model]

4qab: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IWITH 4-(MORPHOLIN-4-YL)-6-[4-(TRIFLUOROMETHYL)PHENYL]PYRIAMINE
Solved by: X-RAY, Resolution: 2.98A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-281 4qabD 17%
[Model]
78-281 4qabE 16%
[Model]
76-281 4qabC 16%
[Model]
78-281 4qabB 16%
[Model]
76-281 4qabA 16%
[Model]
76-281 4qabJ 16%
[Model]
76-281 4qabH 16%
[Model]
76-281 4qabF 16%
[Model]
76-281 4qabI 16%
[Model]
75-281 4qabG 16%
[Model]

4qaa: X-RAY STRUCTURE OF ACETYLCHOLINE BINDING PROTEIN (ACHBP) IWITH 6-(4-METHOXYPHENYL)-N4-OCTYLPYRIMIDINE-2,4-DIAMINE
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

77-281 4qaaD 17%
[Model]
79-281 4qaaB 16%
[Model]
77-281 4qaaC 16%
[Model]
76-281 4qaaA 16%
[Model]
77-281 4qaaE 16%
[Model]
77-281 4qaaG 16%
[Model]
76-281 4qaaI 16%
[Model]
76-281 4qaaF 16%
[Model]
77-281 4qaaJ 16%
[Model]
77-281 4qaaH 16%
[Model]

3u8n: CRYSTAL STRUCTURE OF THE ACETYLCHOLINE BINDING PROTEIN (ACLYMNAEA STAGNALIS IN COMPLEX WITH NS3950 (1-(6-BROMO-5-ET3-YL)-1,4-DIAZEPANE)
Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

78-281 3u8nD 17%
[Model]
78-281 3u8nB 16%
[Model]
78-281 3u8nC 17%
[Model]
77-281 3u8nA 16%
[Model]
78-281 3u8nE 16%
[Model]
77-283 3u8nF 16%
[Model]
77-283 3u8nI 16%
[Model]
78-281 3u8nJ 16%
[Model]
78-281 3u8nH 16%
[Model]
78-281 3u8nG 16%
[Model]
77-283 3u8nK 16%
[Model]
77-282 3u8nM 16%
[Model]
78-281 3u8nN 16%
[Model]
78-281 3u8nL 16%
[Model]
78-281 3u8nO 16%
[Model]
78-282 3u8nQ 16%
[Model]
77-283 3u8nP 16%
[Model]
77-283 3u8nS 16%
[Model]
78-281 3u8nR 16%
[Model]
78-281 3u8nT 16%
[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.