SWISS-MODEL Repository - Model Details

Model Overview
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1
240

Sequence
UniProt O43557
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
O43557: 9606.ENSP0000024

Domain
Link to: [ InterPro ]
TNF

Model 3D Structure
Model information:
Modelled residue range: 93 to 240
Based on template: [ 4en0 ]  
Sequence Identity [%]: 97%
Model date: 2013-02-18
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (4en0): TRIMER
Model: TRIMER

Ligand information: [details]
Ligands in the template: GOL: 1, NAG: 1, PO4: 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 2013-01-30. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment 

TARGET    1       NPAAHLTG ANSSLTGSGG PLLWETQLGL AFLRGLSYHD GALVVTKAGY
4en0_1#9  93      npaahltg anssltgsgg pllwetqlgl aflrglsyhd galvvtkagy
                                                                      
TARGET             sssssss s   hh       sss       sss  sss   ssss   ss
4en0_1#9           sssssss s   hh       sss       sss  sss   ssss   ss


TARGET    49    YYIYSKVQLG GVGCPLGLAS TITHGLYKRT PRYPEELELL VSQQSPCGRA
4en0_1#9  141   yyiyskvqlg gvgcplglas tithglykrt prypeelell vsqqspcgra
                                                                      
TARGET          ssssssssss s           ssssssss        ssss ssss      
4en0_1#9        ssssssssss s           ssssssss        ssss ssss      


TARGET    99    TSSSRVWWDS SFLGGVVHLE AGEKVVVRVL DERLVRLRDG TRSYFGAFMV
4en0_1#9  191   t---rvwwds sflggvvhle ageevvvrvl derlvrlrdg trsyfgafmv
                                                                      
TARGET                ssss sssssssss    ssssssss        hhh hh sssssss
4en0_1#9              ssss sssssssss    ssssssss        hhh hh sssssss


TARGET    149    - VNPAAHL TGANSSLTGS GGPLLWETQL GLAFLRGLSY HDGALVVTKA
4en0_1#9  92    ---vnpaahl tganss---s ggpllwetql glaflrglsy hdgalvvtka
                 *                                                    
TARGET               sssss ss                sss  sssss  ss s  ssss   
4en0_1#9             sssss ss                       sss  ss s  ssss   


TARGET    196   GYYYIYSKVQ LGGVGCPLGL ASTITHGLYK RTPRYPEELE LLVSQQSPCG
4en0_1#9  139   gyyyiyskvq lggvgcpl-- -stithglyk rtprypeele llvsqqspcg
                                                                      
TARGET          ssssssssss sssss         sssssss s       ss ssssss    
4en0_1#9        ssssssssss sssss         sssssss s       ss ssssss    


TARGET    246   RATSSSRVWW DSSFLGGVVH LEAGEKVVVR VLDERLVRLR DGTRSYFGAF
4en0_1#9  189   ratsssrvww dssflggvvh leageevvvr vlderlvrlr dgtrsyfgaf
                                                                      
TARGET                ssss ssssssssss s   ssssss ss   sss       ssssss
4en0_1#9              ssss ssssssssss s   ssssss ss   sss       ssssss


TARGET    296   MV - VNPAA HLTGANSSLT GSGGPLLWET QLGLAFLRGL SYHDGALVVT
4en0_1#9  239   mv---vnpaa hltganss-- ---gpllwet qlglaflrgl syhdgalvvt
                   *                                                  
TARGET          ss     sss ss                         sss   sss  ssss 
4en0_1#9        ss     sss ss                         sss   sss  ssss 


TARGET    343   KAGYYYIYSK VQLGGVGCPL GLASTITHGL YKRTPRYPEE LELLVSQQSP
4en0_1#9  137   kagyyyiysk vqlggvgcpl glastithgl ykrtprypee lellvsqqsp
                                                                      
TARGET            ssssssss sssss           sssss sss        ssssssss  
4en0_1#9          ssssssss sssss           sssss sss        ssssssss  


TARGET    393   CGRATSSSRV WWDSSFLGGV VHLEAGEKVV VRVLDERLVR LRDGTRSYFG
4en0_1#9  187   cgratsssrv wwdssflggv vhleageevv vrvlderlvr lrdgtrsyfg
                                                                      
TARGET                     ssssssssss sss   ssss ssss   sss      sssss
4en0_1#9                   ssssssssss sss   ssss ssss   sss      sssss


TARGET    443   AFMV                                                  
4en0_1#9  237   afmv-                                                 
                                                                      
TARGET          ssss                                                  
4en0_1#9        ssss

Quality 


Template's ligands section 
Ligands in the template: GOL: 1, NAG: 1, PO4: 1. 
Ligands in the template that will be assessed: NAG3. 
Model's ligands section 
NAG3 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand z.NAG3 will not be included in the model. 
NAG3: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 4en0 is annotated as 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: 4en0.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=TRIMER) 
 The corresponding reliability score is 0.828 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 4en0C 4en0B  
 Model was succesfully built as TRIMER.

Template Selection 
 - Start SMR-Pipeline for:4c17e15c57225fa9b4d0659c15e9561c on BC2-cluster at Mon Feb 18 01:08:23
2013 


 - 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

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with R found
 - No template with S found
 - No template with T found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with A found
 - No template with A found
 - No template with A found
 - No template with D found
 - No template with D found
 - No template with D found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with R found
 - No template with S found
 - No template with T found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with G found
 - No template with H found
 - No template with I found
 - 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 4en0A (93-240) 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:4c17e15c57225fa9b4d0659c15e9561c on BC2-cluster at Mon Feb 18 01:12:05
2013


Template Description
Match Chain SeqId

4en0: CRYSTAL STRUCTURE OF LIGHT
Solved by: X-RAY, Resolution: 2.59A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

93-240 4en0A 97%
[Model]
92-240 4en0C 96%
[Model]
92-240 4en0B 95%
[Model]

4f3j: CRYSTAL STRUCTURE OF TRIMERIC GC1Q DOMAIN OF HUMAN C1QTNF5WITH LATE-ONSET RETINAL MACULAR DEGENERATION
Solved by: X-RAY, Resolution: 1.34A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

109-240 4f3jA 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.