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 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 ]
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Alignment
TARGET 1 GVC SMMRLPLQSS ---PEGLDAA FIGVPLDTGT
3nioD 4 nlhqplggne mprfg--gia tmmrlphvqs paeldaldaa fvgvpldigt
TARGET sss ssss
3nioD hhhhh sss ssss
TARGET 31 SNRPGARFGP CRIREESLML GAVNPSTGAL PFQSLRVADL GNVNVNLYNL
3nioD 52 slrsgtrfgp reiraesvmi rpynmatgaa pfdslnvadi gdvaintfnl
TARGET h hhhhh h
3nioD h hhhhh hhh h
TARGET 81 QDSCLLIREA YQNVLAAGCI PLTLGGDQTI TYPILQAVAK EHGPVGLVHV
3nioD 102 leavriieqe ydrilghgil pltlggdhti tlpilrai-- khg-vglvhv
TARGET hhhhhhhhhh hhhhhh s sssss hh hhhhhhh sssss
3nioD hhhhhhhhhh hhhhhh s sssss hh hhhhhhh sssss
TARGET 131 GAHTNTTDKP REEKVYHRTP FRRSVDEGLL DSKRVVQIGI RGSSRTLDPY
3nioD 152 dahadvndhm fge-iahgtt frraveedll dcdrvvqigl raqgytaedf
TARGET s hhhhhhh ssssss hhh
3nioD s h hhhhhh ssssss hhh
TARGET 181 RYSRSQGFRV VLAEDCWMKS LVPLMAEVRQ QMGGKPLYIS FAIDALDPAY
3nioD 202 nwsr-qgfrv vqaeecw-hs leplmaevre -vgggpvyls fdidgidpaw
TARGET hhhhhh ss s hhhh hhhhhhhh sssss sss
3nioD hh ss s hhh hhhhhhh sssss sss
TARGET 231 APGTGTPEIA GLTPSQALEI IRGCQGLNVV GCDLVEVSPP YDLSGNTALL
3nioD 252 apgtgtpeig glttiqamei irgcqgldli gcdlvevspp ydttgntsll
TARGET hhhhhhh hhh sssss hhhhh
3nioD hhhhhhh hhh sssss hhhhh
TARGET 281 AANLLFEMLC ALPKV --
3nioD 302 ganllyemlc vlpgvvrr
TARGET hhhhhhhhhh
3nioD hhhhhhhhhh
Template's ligands section
Ligands in the template:ALA : 7,LYS : 1,MN : 2.
Ligands in the template that will be assessed: MN1607, MN1608.
Model's ligands section
MN1607
One or more ligand's atoms are closer than 1.5 Angstroem to one or more atoms that belong to the model or to other ligands.
Given the properties calculated previously, the ligand D.MN1607 will not be included in the final model.
MN1607: conservation:False, RMSD:False, included: False
MN1608
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand D.MN1608 will not be included in the final model.
MN1608: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3nio is annotated as HEXAMER
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: 3nio.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 (=HEXAMER)
The corresponding reliability score is 0.766 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 3nioC 3nioF 3nioB 3nioE 3nioA
Unfortunately, we were not able to built the model as HEXAMER.
Thus, the model was built as single chain.
Template Selection
- Start SMR-Pipeline for:33d3b88821ac401bea467807b54d1adf on BC2-cluster at Fri Feb 22 22:35:25
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
- Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
- 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
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ******************************************************************
- Oligomeric modeling of 3nioD was not successful, fall back to monomeric modeling
- building model based on 3nioD (61-355) 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:33d3b88821ac401bea467807b54d1adf on BC2-cluster at Fri Feb 22 23:09:39
2013
Template Search
| Template Description |
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3nio: CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA GUANIDINOBUTYR Solved by: X-RAY, Resolution: 2.00A, Identified by BLAST |
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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.