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 I PTCKITLKET FLTSPEELYR VFTTQELVQA FTHAPAALEA
1x53_1#2 1 gssgssg--i ptckitlket fltspeelyr vfttqelvqa fthapatlea
TARGET ssssssssss s hhhhhh h hhhhhh hh ssss
1x53_1#2 ssssssssss s hhhhhh h hhh hh
TARGET 42 DRGGKFHMVD GNVTGEFTDL VPEKHIAMKW RFKSWPEGHF ATITLTFIDK
1x53_1#2 49 drggkfhmvd gnvsgeftdl vpekhivmkw rfkswpeghf atitltfidk
TARGET s sssssss sssssssss s sssssss sssssss
1x53_1#2 ssssss sssssssss s sssssss sssssss
TARGET 92 NGETELCMEG RGIPAPEEER TRQGWQRYYF EGIKQTFGYG A -----
1x53_1#2 99 ngetelcmeg rgipapeeer trqgwqryyf egikqtfgyg asgpssg
TARGET sssssss sssss hh hhh h hhhhhh
1x53_1#2 sssssss sssss hh hhh h hhhhhhh
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1x53 is annotated as MONOMER
The template structure (1x53) was solved by NMR and does not contain any quaternary structure annotation
The template is annotated by the number of chains found in the PDB file
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 0.634 (>0.5 indicates similarity)
Model was succesfully built as MONOMER.
Template Selection
- Start SMR-Pipeline for:a28484e8cd4bd1731b872a1103676572 on BC2-cluster at Fri Feb 22 13:59:45
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 1
- But still uncovered regions of the target sequence detected, go for: HHSEARCH
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- No template with E 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 1x53A (204-335) was successful
- ************************
- building model based on 1usvF (25-126) 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:a28484e8cd4bd1731b872a1103676572 on BC2-cluster at Fri Feb 22 14:01:03
2013
Template Search
| Template Description |
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1x53: THE SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN ACTIVATOR OF 90 KDA HEAT SHOCK PROTEIN ATPASE HOMOLOG 1 Solved by: NMR, Identified by BLAST |
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1xfs: X-RAY CRYSTAL STRUCTURE OF PROTEIN NE0264 FROM NITROSOMONAEUROPAEA. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGETNER5. Solved by: X-RAY, Resolution: 1.70A, Identified by HHSEARCH |
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2ns9: CRYSTAL STRUCTURE OF PROTEIN APE2225 FROM AEROPYRUM PERNIXK1, PFAM COXG Solved by: X-RAY, Resolution: 1.80A, 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.