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 MFT SVAQANAAVI EQIRRARPHW LDVQPASSLI SELNEGKTLL
3clqB 54 snapt--lye kiqqaneeav triiqskpil vgfdkainvx pdxte-ttil
TARGET hh hhhhhhhhhh hhhhh ssss ssssss
3clqB hhh hhhhhhhhhh hhhhh ssss ssssss
TARGET 44 HAGPPMRWQE MTGPMKGACV GACLFEGWAK DEAQALAILE QGEVNFIPCH
3clqB 101 hagppityen xcgpxkgavq galvfeglak dladadrvar sgaitfspch
TARGET hhhhhhhh hhhhhh hhhhhhhhh
3clqB hhhhhhhh hhhhhh hhhhhhhhh
TARGET 94 HVNAVGPMGG ITSASMPMLV VENVTDGNRA YCNLNEGIGK VMRFGAYGED
3clqB 151 ehdavgsxag vtspnxyvhi iknetygnta ftnlseqlak vlrfgandqs
TARGET sssss ssss sss ss hh
3clqB sssss ssss sss ss hh
TARGET 144 VLTRHRWMRD VLMPVLSAAL GRMERGIDLT AMMAQGITMG DEFHQRNIAS
3clqB 201 vvdrliwxrd vlgpllhdax tfcpegidlr lxlsqalhxg dechnrnvag
TARGET hhhhhhhhh hhhhhhhh sssh hhhhhhhh hhh
3clqB hhhhhhhhh hhhhhhhh sssh hhhhhhhh hhh
TARGET 194 SALLMRALAP QIARLDHDKQ HIAEVMDFLS VTDQFFLNLA MAYCKAAMDA
3clqB 251 stllvqaltp yxvqtdfsre qlkevfeflg ssdyfsgptw xgaakcalda
TARGET hhhhhhhhhh hhh hh hhhhhhhhh hhh hhhhhhhhhh
3clqB hhhhhhhhhh hhh hh hhhhhhhhh hhh hhhhhhhhhh
TARGET 244 GAMIRAGSIV TAMTRNGNMF GIRVS-GLGE RWFTAPVNTP QGLFFTGFSQ
3clqB 301 ghnvenstiv ttxcrngvef girvsgiggn hwftgpaqrv igpxfagytq
TARGET h sss ssssssssss sssss sssss sssss
3clqB h sss s sssssss sssss sssss sssss
TARGET 293 EQANPDMGDS AITETFGIGG AAMIAAPGVT RFVGAGGMEA ARAVSEEMAE
3clqB 351 edagldxgds aitetygvgg faxaaapaiv plvg-gtvae alnyskexle
TARGET sss sss h hhhhhh h h hhh hhh hhh hhhhhhhhhh
3clqB sss sss hhhh hhh hhh hhh hhhhhhhhhh
TARGET 343 IYLERNMQLQ IPSWDFQGAC LGLDIRRVVE TGITPLINTG IAHKEAGIGQ
3clqB 400 ittkenpnvt ipvldfxgip tgidvlkvle tgxlpvinta iahkepgigx
TARGET ssssss ss sss ssssss ssssshhhhh h ssss ssss ss
3clqB ssssss ss sss ssssss ssssshhhhh h ssss sssss ssss
TARGET 393 IGAGTVRAPL ACFEQALEAL AESM
3clqB 450 igagltnppa nvfnealkal vatin
TARGET ssssss hhhhhhhhhh hhh
3clqB ssssss hhhhhhhhhh hhh
Template's ligands section
Ligands in the template:PEG : 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
3clq 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: 3clq.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 0.478 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 3clqA
Template Selection
- Start SMR-Pipeline for:f7a4069376b8fbd2c3ca47edaf502f69 on BC2-cluster at Sat Feb 23 06:45:35
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 3clqB (1-416) 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:f7a4069376b8fbd2c3ca47edaf502f69 on BC2-cluster at Sat Feb 23 06:47:40
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.