SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | P0C2F6 |
Database: TrEMBL (Unreviewed)  |
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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 WV KVNTDGASRG N-----PGLA SAGGVLRDCT GAWCG-GFSL
2lsnA 1 gamgqy--eg vfytdgsaik spdptksnna gmgivhatyk peyqvlnqws
TARGET s sssssssss ss ssssssss sss ssss
2lsnA s sssssssss ss sssssss ssss
TARGET 37 N-IGRCSAPQ AELWGVYYGL YFAWEKKVPR VELEVDSEVI VGFLKTGISD
2lsnA 49 iplgnhtaqm aeiaavefac kkalkip-gp vlvitdsfyv aesankelpy
TARGET s ss hhh hhhhhhhhhh hhhh sssss hhh hh
2lsnA sss hhh hhhhhhhhhh hhhh sssss hhh hhhh hhh
TARGET 86 S--------- ---HPLSFLV RLCHGFLQKD WLVRIVHVY- ---------R
2lsnA 98 wksngfvnnk kkplkhiskw ksiaeclsmk pditiqhekg hqptntsiht
TARGET hhh hhhhhhhh sss
2lsnA hh hhhh hhhhhhhh sssss hh
TARGET 114 EANRLADGLA NYAFS --
2lsnA 148 egnaladkla tqgsyvvn
TARGET hhhhhhhh h h
2lsnA hhhhhhhhhh hhhhh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2lsn 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: 2lsn.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 0.1 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:aa37a67e6de8012667cf89378b024390 on BC2-cluster at Wed Feb 20 02:19:05
2013
- 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 (old0 vs new:1): model based on new templates
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *****************
- building model based on 2lsnA (459-586) 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:aa37a67e6de8012667cf89378b024390 on BC2-cluster at Wed Feb 20 02:20:42
2013
Template Search
| Template Description |
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2lsn: SOLUTION STRUCTURE OF PFV RNASE H DOMAIN Solved by: NMR, 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.