SWISS-MODEL Repository 
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SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
Model 3D Structure
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Template Links:
[ RCSB ]
[ PDBe ]
[ SCOP ]
[ CATH ]
display model: in [ AstexViewer ] download model: as [ pdb ] - as [ Deepview project ] 
This model has not been updated since 2012-10-15. 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 ]
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Alignment
TARGET 1 FREAYHW LRENTADDAR VMSWWDYGYQ IAGMANRTTL VDNNTWNNSH
3aagB 436 n--easllnq l-nianredy vvtwwdygyp vryysdv-tl vdgg-hlgd-
TARGET hh h h h hh h
3aagB hh s ss h hh h
TARGET 48 IALVGKAMSS NESAAYEIMT ELDVDY --- ---------- ----------
3aagB 484 nffpsfal-s deqaaanxar l-sveytesf laslspdfid tptrdiylyx
TARGET hhhhhhh hhhhhh
3aagB hhhhhh hhhhh h h hhhh hh sss
TARGET ---------- ---------- ---------- ---------- ----------
3aagB 565 parxslifst vasfsfpftf staypldvng eiylsngvvl sddfrsfigv
TARGET
3aagB hh hh ss ssssss s sssss sss ss sss
TARGET ---------- ---------- ---------- ---------- ----------
3aagB 629 vsvnsivein siqgeyitpi ddaqfyifyl dsaipyaqfi lxdtxfnsay
TARGET
3aagB sssssssss sss sssss s sss sss hh
TARGET ---------- ---------- -----
3aagB 684 vqxfflgnyn lfdlvinsrd avfli
TARGET
3aagB hhhhh
Template's ligands section
Ligands in the template:ALA : 19,ILE : 1,LEU : 1,SER : 1.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3aag is annotated as MONOMER
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: 3aag.pdb2.gz
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 26.027) 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
Template Selection
- Start SMR-Pipeline for:1a7936b51e2b455f0b37d42ad4918fd2 on BC2-cluster at Tue Oct 30 23:39:24
2012
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old2 vs new:3): model based on new templates
- Send 3 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ***********************
- Oligomeric modeling of 2lgzA was not successful, fall back to monomeric modeling
- building model based on 2lgzA (496-717) was not successful go to next best template
- ****************************
- Oligomeric modeling of 2lgzA was not successful, fall back to monomeric modeling
- building model based on 2lgzA (490-752) was not successful go to next best template
- ********
- building model based on 3aagB (527-599) was successful
- *********************
- Oligomeric modeling of 3vgpA was not successful, fall back to monomeric modeling
- building model based on 3vgpA (521-716) was not successful go to next best template
- ****************************************************************
- building model based on 3rceA (22-631) 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:1a7936b51e2b455f0b37d42ad4918fd2 on BC2-cluster at Tue Oct 30 23:43:27
2012
Template Search
| Template Description |
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2lgz: SOLUTION STRUCTURE OF STT3P Solved by: NMR, Identified by HHSEARCH |
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3aag: CRYSTAL STRUCTURE OF C. JEJUNI PGLB C-TERMINAL DOMAIN Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH |
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2zai: CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF STT3 FROM P. FURIOSUS Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH |
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2zag: CRYSTAL STRUCTURE OF THE SEMET-SUBSTITUTED SOLUBLE DOMAIN OF STT3 FROM P. FURIOSUS Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH |
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3vgp: CRYSTAL STRUCTURE OF THE C-TERMINAL GLOBULAR DOMAIN OF OLIGOSACCHARYLTRANSFERASE (AF_0329) FROM ARCHAEOGLOBUS FU Solved by: X-RAY, Resolution: 1.75A, Identified by HHSEARCH |
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3rce: BACTERIAL OLIGOSACCHARYLTRANSFERASE PGLB Solved by: X-RAY, Resolution: 3.40A, Identified by HHSEARCH |
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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.