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 AAAKYEKK SPTEHVLLRP DTYIGGVAMR EDQIIWLRDS ENRKMIAKEV
1pvgB 8 asdkyqki sqlehilkrp dtyigsvetq e-qlqwiyde etdcxieknv
TARGET hhhhhh hhh sssssss sssssss
1pvgB hhhhhh hhh s s sssssss sssssss
TARGET 49 TYPPGLLKIF DEILVNAADN KARDSSMNRL EVWLDRETAR ISVWNNGSGL
1pvgB 55 tivpglfkif deilvnaadn kvrdpsxkri dvnihaeeht ievkndgkgi
TARGET hhhhhhh hhhhhhhhhh hhh sss ssssss ss sssss
1pvgB ss hhhhhhh hhhhhhhhhh hhh sss ssssss ss ssssss
TARGET 99 PVEIHPTEGI YVPTLVFGNL FTSSNYDDSE IKTVGGRNGY GAKLCNIFSK
1pvgB 105 pieihnkeni yipexifghl ltssnyddde kkvtggrngy gaklcnifst
TARGET hhhhh hhhhhhhsss
1pvgB hhhhh hhhhhhhsss
TARGET 149 EFIVETVDTR IKRRFRQKWY DNMKKCNEAE VVEILDETVK DYTKVEFVPD
1pvgB 155 efiletadln vgqkyvqkwe nnxsichppk itsy--kkgp sytkvtfkpd
TARGET ssssssss sssssssss ss ssss s ssss sssssssss
1pvgB ssssssss sssssssss ss ssss s ssss sssssssss
TARGET 199 LERFQIDKLS DDVIDLIGRR VFEVAATLPR DVDVYLNGQK CDVDGFEDYV
1pvgB 203 ltrfgxkeld ndilgvxrrr vydingsv-r dinvylngks lkirnfknyv
TARGET hhh hhhhhhhhhh hhhhhhh sssss ss s hhhhh
1pvgB hhh hhhhhhhhhh hhhhhhh sssss ss s hhhhh
TARGET 249 KMFNDSS--- SLLFLHPTPR WHVGVAKRNN FFGESHVVLP KIVSFVNNIN
1pvgB 252 elylksleip tilyerinnr wevafavsdi sfqq------ --isfvnsia
TARGET hh sss s ssssssss sssss ss
1pvgB h hhh sssss s ssssssss ss sssss ss
TARGET 296 TEKGGSHVDY VMDKIVNIIK PIVDSKLGDP TKSVKPAVIK NNLSIFINCL
1pvgB 310 ttxggthvny itdqivkkis eil------- kksvksfqik nnxfifincl
TARGET s hhhhh hhhhhhhhhh h hhhh sssssssss
1pvgB s hhhhh hhhhhhhhhh hhh h hhhh hsssssssss
TARGET 346 IENPSFESQT KETLTTKAKN FGS ------ ---------- ---------
1pvgB 357 ienpaftsqt keqlttrvkd fgsrceiple yinkixktdl atrxfeiad
TARGET sssss sssss hh
1pvgB sssss sssss hh h hhhhhh h hhhhhhhh
Template's ligands section
Ligands in the template:ANP : 1,MG : 1.
Ligands in the template that will be assessed: ANP902, MG904.
Model's ligands section
ANP902
ANP902 interacts, within a radius of 3 Angstroem, with the following ions: MG904. They will be considered as a single ligand.
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.060
Given the properties calculated previously, the ligand ANP902 will be included in the model.
ANP902: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
1pvg is annotated as DIMER
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: 1pvg.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 (=DIMER)
The corresponding reliability score is 0.624 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1pvgA
Unfortunately, we were not able to built the model as DIMER.
Thus, the model was built as single chain.
Template Selection
- Start SMR-Pipeline for:830fd97f832a946fc14007227c7d6059 on BC2-cluster at Wed Feb 13 21:00:57
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
FATAL - No A3m found
- Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
- No template with C found
- No template with D 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 C found
- No template with D found
- No template with A found
- No template with B found
- No template with B found
- No template with C found
- No template with D found
- No template with A found
- No template with A found
- No template with B found
- No template with C found
- No template with A found
- No template with B found
- No template with D found
- No template with C found
- No template with D found
- No template with A found
- No template with B found
- No template with B found
- No template with B found
- No template with A found
- No template with A 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 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 C found
- No template with D 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
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:3): model based on new templates
- Send 3 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *************************
- Oligomeric modeling of 1pvgB was not successful, fall back to monomeric modeling
- building model based on 1pvgB (43-410) was successful
- ************************************************
- Oligomeric modeling of 4fm9A was not successful, fall back to monomeric modeling
- building model based on 4fm9A (454-1162) was not successful go to next best template
- ************************************************
- building model based on 3l4jA (452-1157) was not successful go to next best template
- ****************************************************************************
- building model based on 4gfhF (43-1157) was not successful go to next best template
- ****************************************************************************
- building model based on 4gfhA (43-1157) was not successful go to next best template
- ************************************************
- building model based on 3l4kA (452-1157) was not successful go to next best template
- ************************************************
- building model based on 2rgrA (452-1157) 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:830fd97f832a946fc14007227c7d6059 on BC2-cluster at Wed Feb 13 21:54:21
2013
Template Search
no data available!
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.