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 ELDDIF ISVKTTKNYH DTRLALIIKT WFQLARDQTW FFTDTDDHYY
2j0aA 50 el--qlgdif iavkttwafh rsrldllldt wvsrirqqtf iftdspderl
TARGET sss sssss hhhh hh sss sss hhh
2j0aA sss sssss hhhh hh sss sss hhh
TARGET 47 QEKTKGHLIN TKCSQGHFRK ALCCKMSAEL DVFLESGKKW FCHFDDDNYV
2j0aA 98 qerlgphlvv tqc------- alsckmaaef daflvsglrw fchvdddnyv
TARGET hhh ssss s hhhhhhh hhhhh ss ssssss ss
2j0aA hhh ssss s hhhhhhh hhhhh ss ssssss ss
TARGET 97 NVPRLVKLLD EYSPSVDWYL GKPSISSPLE IHLDSKNTTT NKKITFWFAT
2j0aA 148 npkallqllk tfpqdrdvyv gkpsl----- ---------- -----fwfat
TARGET shhhhhhhhh sss ssss sss
2j0aA shhhhhhhhh sss ssss sss
TARGET 147 GGAGFCLSRA LTLKMLPIAG GGKFISIGDK IRFPDDVTMG FIIEHLLKVP
2j0aA 197 ggagfcinrq lalkmvpwas gshfvdtsal irlpddctvg yiiecklggr
TARGET sssssh hhhhhhhhh hhh hhhhhh hhhhh
2j0aA sssssh hhhhhhhhh hhh hhhhhh hhhhhh
TARGET 197 LTVVDNFHSH LEPMEFIRQD TFQDQVSFSY AHMKNQWNVI KVDG-FDMKT
2j0aA 247 lqpsplfhsh letlqllgaa qlpeqvtlsy gvfegklnvi klpgpfshee
TARGET sss h hhh sss sss sss
2j0aA sss hh hhh sss sss sss
TARGET 246 DPKRFYSLHC QLFPYFSFCP -
2j0aA 297 dpsrfrslhc llypdtpwcp ll
TARGET hhhhhh hh
2j0aA hhhhhh hh
Template's ligands section
Ligands in the template:K : 1,SO4 : 1.
Ligands in the template that will be assessed: K1320.
Model's ligands section
K1320
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 A.K1320 will not be included in the final model.
K1320: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2j0a 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: 2j0a.pdb1.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.178 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:6ac109497e1d3f6c336d9a75ac377597 on BC2-cluster at Fri Feb 22 07:53:18
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
- 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 2j0aA (146-410) 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:6ac109497e1d3f6c336d9a75ac377597 on BC2-cluster at Fri Feb 22 07:55:18
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.