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
3fpfB 2 scyiywdkik riasrlegmn yhfdemdtsg vmplldeiee iahdstidfe
3fpfB hhhhhh hhhhhhhhhh hh hh hhhhhhhh hh hh
TARGET 1 DNPLHHLN
3fpfB 52 sakhilddae mnhalslirk fyvnlgmkle mekaqevies --dspwetlr
TARGET hhhhhh
3fpfB hhhhhh hhhhhhhh hhhhhhhhhh hhhhhhhhh hhhhhh
TARGET 9 IFPYYNNYLK LGKLEFDLLE QNLNGFVPKS VAFIGSGPLP LTSIVLASFH
3fpfB 100 sfyfypryle llkneaalgr frrg----er avfigggplp ltgills--h
TARGET hhhhhhh hhhhhhh ss sssss hhhhhh
3fpfB hhhhhhh hhhhhhhhh ss sssss hhhhhhh h
TARGET 59 LKDTIFHNFD IDPSANSLAS LLVSSDPDIS QRMFFHTVDI MDVTESL---
3fpfB 144 vygmrvnvve iepdiaelsr kvieg----- --lgvdgvnv itgdetvidg
TARGET ssssss hhhhhhhh h hhh ssss sss
3fpfB hh ssssss hhhhhhhh hhhhh h ssss sss hhhh
TARGET 106 KSFDVVFLAA LVGMNKEEKV KVIEHLQKHM APGAVLMLRS AHGPRAFLYP
3fpfB 187 lefdvlmvaa la----epkr rvfrnihryv dtetriiyrt ytgmrailya
TARGET sssss hh hhhhhhh ssssss hhh
3fpfB sssss hh hhhhhhh ssssss
TARGET 156 IVEPCDLQGF EVLSIYHPTD DVINSVVISK KHP
3fpfB 233 pvsddditgf rragvvlpsg kvnntsvlvf kcp-
TARGET ss ssssss ssssss ss
3fpfB ss ssssss ssssss ss
Template's ligands section
Ligands in the template:MTA : 1,TNA : 1.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3fpf 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: 3fpf.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 (=DIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.22 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 3fpfA
Template Selection
- Start SMR-Pipeline for:d202b96bf2ee77d1d2063e42dc0815bf on BC2-cluster at Tue Feb 19 21:43:05
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:
- No template with A found
- No template with G found
- No template with H found
- No template with E found
- No template with F found
- No template with B found
- No template with C found
- No template with D found
- No template with B found
- No template with D found
- No template with B found
- No template with C found
- No template with B found
- No template with C found
- No template with B found
- No template with C found
- No template with B found
- No template with C 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 3fpfB (89-276) was successful
- *********************************************************
- building model based on 4g56C (9-235) was not successful go to next best template
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- building model based on 4gqbA (9-235) was not successful go to next best template
- *****************************************************
- building model based on 4g56A (25-235) was not successful go to next best template
- 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:d202b96bf2ee77d1d2063e42dc0815bf on BC2-cluster at Tue Feb 19 21:46:31
2013
Template Search
| Template Description |
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4htf: CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE-DEPENDENT METHYLFROM ESCHERICHIA COLI IN COMPLEX WITH S-ADENOSYLMETHIONIN Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH |
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3ou2: DHPI-SAH COMPLEX STRUCTURE Solved by: X-RAY, Resolution: 1.50A, Identified by HHSEARCH |
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3ou6: DHPI-SAM COMPLEX Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH |
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4hc4: HUMAN HMT1 HNRNP METHYLTRANSFERASE-LIKE PROTEIN 6 (S. CERE Solved by: X-RAY, Resolution: 1.97A, Identified by HHSEARCH |
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3ou7: DHPI-SAM-HEP COMPLEX Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH |
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4a6d: CRYSTAL STRUCTURE OF HUMAN N-ACETYLSEROTONIN METHYLTRANSFERASE (ASMT) IN COMPLEX WITH SAM Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH |
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4a6e: CRYSTAL STRUCTURE OF HUMAN N-ACETYLSEROTONIN METHYLTRANSFE(ASMT) IN COMPLEX WITH SAM AND N-ACETYLSEROTONIN Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH |
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4hg2: THE STRUCTURE OF A PUTATIVE TYPE II METHYLTRANSFERASE FROMANAEROMYXOBACTER DEHALOGENANS. Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH |
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4g56: CRYSTAL STRUCTURE OF FULL LENGTH PRMT5/MEP50 COMPLEXES FROLAEVIS Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH |
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4gqb: CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX Solved by: X-RAY, Resolution: 2.06A, Identified by HHSEARCH |
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2igt: CRYSTAL STRUCTURE OF THE SAM DEPENDENT METHYLTRANSFERASE FROM AGROBACTERIUM TUMEFACIENS Solved by: X-RAY, Resolution: 1.89A, Identified by HHSEARCH |
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3hm2: CRYSTAL STRUCTURE OF PUTATIVE PRECORRIN-6Y C5,15- METHYLTRANSFERASE TARGETED DOMAIN FROM CORYNEBACTERIUM DIPHTHERIAE Solved by: X-RAY, Resolution: 2.21A, Identified by HHSEARCH |
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3vyw: CRYSTAL STRUCTURE OF MNMC2 FROM AQUIFEX AEOLICUS Solved by: X-RAY, Resolution: 2.49A, 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.