SWISS-MODEL Repository - Model Details

Model Overview
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1
69

Sequence
UniProt O14610
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
O14610: 9606.ENSP0000030

Domain
Link to: [ InterPro ]
G-gamma

Model 3D Structure
Model information:
Modelled residue range: 5 to 62
Based on template: [ 1got ]  
Sequence Identity [%]: 63%
Model date: 2013-04-22
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (1got): HETERO TRIMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: GDP: 1.
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       LSEKDLLK MEVEQLKKEV KNTRIPISKA GKEIKEYVEA QAGNDPFLKG
1gotG     9       ltekdklk mevdqlkkev tlermlvskc ceefrdyvee rsgedplvkg
                                                                      
TARGET              hhhhhh hhhhhhhhhh       hhhh hhhhhhhhh       hhhh 
1gotG               hhhhhh hhhhhhhhh        hhhh hhhhhhhhh       hhhh 


TARGET    49    IPEDKNPFKE                                            
1gotG     57    ipedknpfke -                                          
                                                                      
TARGET                                                                
1gotG

Quality 


Template's ligands section 
Ligands in the template: GDP: 1. 
Ligands in the template that will be assessed: GDP355. 
Model's ligands section 
GDP355 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand G.GDP355 will not be included in the model. 
GDP355: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 1got is annotated as HETERO TRIMER 
 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: 1got.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 1got_1

Template Selection 
 - Start SMR-Pipeline for:858b36282e0747c2c7fceca62beedf72 on BC2-cluster at Sun Apr 21 22:40:28
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

 - No A3m found

 - No template with A found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with C found
 - No template with B found
 - No template with P found
 - No template with B found
 - No template with P found
 - No template with A found
 - No template with C found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -       *******************************************************************
 - building model based on 1gotG (5-62) 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:858b36282e0747c2c7fceca62beedf72 on BC2-cluster at Sun Apr 21 22:40:57
2013


Template Description
Match Chain SeqId

1got: HETEROTRIMERIC COMPLEX OF A GT-ALPHA/GI-ALPHA CHIMERA AND THE GT-BETA-GAMMA SUBUNITS
Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

5-62 1gotG 64%
[Model]

1tbg: BETA-GAMMA DIMER OF THE HETEROTRIMERIC G-PROTEIN TRANSDUCI
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-62 1tbgE 63%
[Model]
3-61 1tbgH 63%
[Model]
3-61 1tbgG 63%
[Model]
3-61 1tbgF 63%
[Model]

2trc: PHOSDUCIN/TRANSDUCIN BETA-GAMMA COMPLEX
Solved by: X-RAY, Resolution: 2.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-62 2trcG 63%
[Model]

1b9y: STRUCTURAL ANALYSIS OF PHOSDUCIN AND ITS PHOSPHORYLATION- REGULATED INTERACTION WITH TRANSDUCIN BETA-GAMMA
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-62 1b9yB 63%
[Model]

1b9x: STRUCTURAL ANALYSIS OF PHOSDUCIN AND ITS PHOSPHORYLATION- REGULATED INTERACTION WITH TRANSDUCIN
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-62 1b9xB 63%
[Model]

1a0r: HETEROTRIMERIC COMPLEX OF PHOSDUCIN/TRANSDUCIN BETA-GAMMA
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-62 1a0rG 63%
[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.