SWISS-MODEL Repository - Model Details

Model Overview
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1
109

Sequence
UniProt O02495
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
O02495: 6239.T10H9.4

Domain
Link to: [ InterPro ]
Synaptobrevin

Model 3D Structure
Model information:
Modelled residue range: 23 to 52
Based on template: [ 3rk2 ]  
Sequence Identity [%]: 90%
Model date: 2013-05-06
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (3rk2): HETERO TETRAMER
Model built :SINGLE CHAIN

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       RLQQTQAQ VDEVVGIMKV NVEKVLERDQ KL                   
3rk2A     31      rlqqtqaq vdevvdimrv nvdkvlerdq kl-                  
                                                                      
TARGET              hhhhhh hhhhhhhhhh hhhhhhhhhh hh                   
3rk2A               hhhhhh hhhhhhhhhh hhhhhhhhhh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3rk2 is annotated as HETERO TETRAMER 
 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: 3rk2.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3rk2_1

Template Selection 
 - Start SMR-Pipeline for:a8a4a157dd63bbdc2dbbe6bfb6d5889e on BC2-cluster at Mon May  6 14:37:44
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  2 go for
modeling ...

 - No A3m found

 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with B 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 B 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 B found
 - No template with A found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with h found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with g found
 - No template with Z found
 - No template with a found
 - No template with b found
 - No template with m found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with l found
 - No template with R found
 - No template with S found
 - No template with T found
 - No template with k found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with i found
 - No template with d found
 - No template with e found
 - No template with f found
 - No template with n found
 - No template with N found
 - No template with O found
 - No template with P found
 - No template with j found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with B 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 J found
 - No template with K found
 - No template with L 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 3rk2A (23-52) was successful 
 -                ************************************************
 - building model based on 1kilA (20-84) 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:a8a4a157dd63bbdc2dbbe6bfb6d5889e on BC2-cluster at Mon May  6 14:38:43
2013


Template Description
Match Chain SeqId

3rk2: TRUNCATED SNARE COMPLEX
Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

21-52 3rk2E 88%
[Model]
23-52 3rk2A 90%
[Model]

1kil: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEXIN/SNARE COMPLEX
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

20-84 1kilA 88%
[Model]

3rk3: TRUNCATED SNARE COMPLEX WITH COMPLEXIN
Solved by: X-RAY, Resolution: 3.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

20-52 3rk3A 88%
[Model]

3rl0: TRUNCATED SNARE COMPLEX WITH COMPLEXIN (P1)
Solved by: X-RAY, Resolution: 3.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

20-52 3rl0A 88%
[Model]
20-52 3rl0E 88%
[Model]
20-52 3rl0I 88%
[Model]
17-52 3rl0M 83%
[Model]
20-52 3rl0Q 88%
[Model]
20-52 3rl0U 88%
[Model]
20-52 3rl0Y 88%
[Model]
20-52 3rl0c 88%
[Model]

3fie: CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE F CATALYTIC DOMAIN WITH AN INHIBITOR (INH1)
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

20-49 3fieC 87%
[Model]
20-49 3fieD 87%
[Model]

1n7s: HIGH RESOLUTION STRUCTURE OF A TRUNCATED NEURONAL SNARE COMPLEX
Solved by: X-RAY, Resolution: 1.45A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

20-81 1n7sA 87%
[Model]

1sfc: NEURONAL SYNAPTIC FUSION COMPLEX
Solved by: X-RAY, Resolution: 2.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

20-88 1sfcE 87%
[Model]
20-86 1sfcI 87%
[Model]
20-85 1sfcA 86%
[Model]

3ipd: HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, SPACEGROUP I 21 21 21
Solved by: X-RAY, Resolution: 4.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

22-91 3ipdA 86%
[Model]
22-91 3ipdE 86%
[Model]

2kog: LIPID-BOUND SYNAPTOBREVIN SOLUTION NMR STRUCTURE
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

20-91 2kogA 86%
[Model]

3hd7: HELICAL EXTENSION OF THE NEURONAL SNARE COMPLEX INTO THE MEMBRANE, SPACEGROUP C 1 2 1
Solved by: X-RAY, Resolution: 3.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

22-91 3hd7A 86%
[Model]
22-91 3hd7E 86%
[Model]

1l4a: X-RAY STRUCTURE OF THE NEURONAL COMPLEXIN/SNARE COMPLEX FROM THE SQUID LOLIGO PEALEI
Solved by: X-RAY, Resolution: 2.95A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

17-81 1l4aA 75%
[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.