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 T TVLSNNVEMP LIGLGT--TH SGGYYHDAVL HSIKKCGYRL
3f7j_2#3 1 mptslkd--t vklhngvemp wfglgvfkve ngneatesvk aaikn-gyrs
TARGET sss sss sss hhhhhhhh hhhh ss
3f7j_2#3 s s sss ssss s ssss hhhhhhhhh hhhh ss
TARGET 40 IDTAKRYGVE KQLGIAVKNC SVPREEMFLS TKLWPVDCGD EVY-NAFQTS
3f7j_2#3 48 idtaaiykne egvgigikes gvareelfit skvwnedqgy ettlaafeks
TARGET sss h hhhhhhhhh sss sss hhhh
3f7j_2#3 sss h hhhhhhhhh sss sss h hhhhhhhhhh
TARGET 89 CEKLQTDYLD MYMIHMPQLP DWIVNQKETK EKTWRQMELL YEDEHVRSIG
3f7j_2#3 98 lerlqldyld lylihwpg-- ------kdky kdtwralekl ykdgkiraig
TARGET hhhh s sssss h hhhhhhhhhh hhh sss
3f7j_2#3 hhhh s sssss h hhhhhhhhhh hhh sss
TARGET 139 VSNYSIEDLD ELLEFASILP HANQVELHPW FHQADLKNYC DELGILTMGY
3f7j_2#3 140 vsnfqvhhle ellkdaeikp mvnqvefhpr ltqkelrdyc kgqgiqleaw
TARGET sss hhhhh hhh sssss hhhhhhh hhh sssss
3f7j_2#3 sss hhhhh hhh sssssss hhhhhhh hhh sssss
TARGET 189 CPLAKGKYLE DETLCKIASK YQKSPAQICL RWSIQQNVPT VPKSTDCRRL
3f7j_2#3 190 splmqgqlld nevltqiaek hnksvaqvil rwdlqhgvvt ipksikehri
TARGET hhhhhhhhh h hhhhhh hhhhhh s ss hhhh
3f7j_2#3 h hhhhhhhhh h hhhhhh hhhhhh s ss hhhh
TARGET 239 KENTNVFDFE LSAEDMNTLN SFSSQNR -- -------
3f7j_2#3 240 ienadifdfe lsqedmdkid alnkdervgp npdellf
TARGET hhhh hhhhhhhh h
3f7j_2#3 hhh hhhhhhhh h
Template's ligands section
Ligands in the template:K : 2,NO3 : 4.
Ligands in the template that will be assessed: K5, K6.
Model's ligands section
K5
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand z.K5 will not be included in the final model.
K5: conservation:False, RMSD:False, included: False
K6
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand z.K6 will not be included in the final model.
K6: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3f7j 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: 3f7j.pdb2.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 (=MONOMER)
The corresponding reliability score is 0.578 (>0.5 indicates similarity)
Model was succesfully built as MONOMER.
Template Selection
- Start SMR-Pipeline for:c5d45222bdeed1a30835fb36beda0764 on BC2-cluster at Wed Feb 20 20:00:15
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:
- No template with A found
- No template with C found
- No template with D found
- No template with B found
- No template with A found
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:2): model based on new templates
- Send 2 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ******************************************************************
- building model based on 3f7jB (4-268) was successful
- ***********************************************************************
- building model based on 1zuaX (7-290) 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:c5d45222bdeed1a30835fb36beda0764 on BC2-cluster at Wed Feb 20 20:03:32
2013
Template Search
| Template Description |
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4exb: PUTATIVE ALDO-KETO REDUCTASE FROM PSEUDOMONA AERUGINOSA Solved by: X-RAY, Resolution: 2.75A, Identified by HHSEARCH |
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4exa: CRYSTAL STRUCTURE OF THE PA4992, THE PUTATIVE ALDO-KETO REPSEUDOMONA AERUGINOSA Solved by: X-RAY, Resolution: 2.80A, 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.