SWISS-MODEL Repository 
Uniprot features:
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 ] |
Alignment
TARGET 1 IN TVVSCLVFVL GIIGNSTLLR IIYKNKCMRN GPNILIASLA
4djhB 55 spaipv--ii tavysvvfvv glvgnslvmf viirytkmkt atniyifnla
TARGET h hhhhhhhhhh hhhhhhhhhh hhhh hhhhhhhhhh
4djhB hhhh hh hhhhhhhhhh hhhhhhhhhh hhhh hhhhhhhhhh
TARGET 43 LGDLLHIVID IPINVYKLLA EDWPFGAEMC KLVPFIQKAS VGITVLSLCA
4djhB 103 ladal-vttt mpfqstvylm nswpfgdvlc kivlsidyyn mftsiftltm
TARGET hhh hhhhhhhhhh hhhh hhhhhhhhhh hhhhhhhhhh
4djhB hhhhh hhhh hhhhhhhhhh hhhh hhhhhhhhhh hhhhhhhhhh
TARGET 93 LSIDRYRAVA SWSRIKGIGV PKWTAVEIVL IWVVSVVLAV PEAIGFDIIT
4djhB 152 msvdryiavc hpvkaldfrt plkakiinic iwlls----- -ssvgisaiv
TARGET hhhhhhhhh hhhhh hhhhhhhhhh hhh hhhhhh
4djhB hhhhhhhh hhhhhh hhhhhhhhhh hhhhh hhhhhhhhh
TARGET 143 MDYKGSYLRI CLLHPVQKTA FMQFYKTAKD WWL------- FSFYFCLPLA
4djhB 196 lggtkvredv dvie-----c slqfpdddys wwdlfmkicv fifafvipvl
TARGET h hhhhhhh hh hhhh
4djhB sssssss sss s sss hh hhhhhhhhhh hh hhhhh
TARGET 186 ITAFFYTLMT CEMLRKKS - ---------- ---------- ----------
4djhB 241 iiivcytlm- --ilrlksvr llsgnifeml rideglrlki ykdtegyyti
TARGET hhhhhh hhhh
4djhB hhhhhhhhh hhhhhhh hhhhh hhhh sss sss ssss
TARGET ---------- ---------- ---------- ---------- ----------
4djhB 1028 gighlltksp slnaakseld kaigrntngv itkdeaeklf nqdvdaavrg
TARGET
4djhB sss hhhhhhhh ss s hhhhhhhh hhhhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
4djhB 1078 ilrnaklkpv ydsldavrra alinmvfqmg etgvagftns lrmlqqkrwd
TARGET
4djhB hh hhhhh hh hhhhh hhhhhhh hhh hhhh hhhh hhh
TARGET ---------- ---------- ---------- ---------- ----------
4djhB 1128 eaavnlaksr wynqtpnrak rvittfrtgt wdayrekdrn lrritrlvlv
TARGET
4djhB hhhhhhh hhh hhhh hhhhhhhh hhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
4djhB 279 vvavfvvcwt pihifilvea lgstaalssy yfcialgytn sslnpilyaf
TARGET
4djhB hhhhhhh hhhhhhhhhh h hhh hhhhhhhhhh hhhhhhhhh
TARGET ---------- -----
4djhB 333 ldenfkrcfr dfcfp
TARGET
4djhB hhhhhhhh hhh
Template's ligands section
Ligands in the template:JDC : 1,OLC : 2,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
4djh is annotated as DIMER
PISA was used to annotate the quaternary structure, because the author assignment was not complete
A biological unit file could be identified with the same complex description as the PISA annotation and was used to build the assembly: 4djh.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 0.004 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 4djhA
Template Selection
- Start SMR-Pipeline for:0cce1c203fb14e4ae6ca4b8275ed5f91 on BC2-cluster at Sat Apr 20 08:03:57
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- No A3m found
- Run HHSearch to detect more templates...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with C found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with C found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with B found
- No template with A found
- No template with B found
- No template with G found
- No template with N 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 4djhB (103-305) was successful
- ****************************************************
- building model based on 4ea3A (111-398) 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:0cce1c203fb14e4ae6ca4b8275ed5f91 on BC2-cluster at Sat Apr 20 08:10:48
2013
Template Search
| Template Description |
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2lot: AR55 SOLUBILISED IN SDS MICELLES Solved by: NMR, Identified by HHSEARCH |
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2lou: AR55 SOLUBILISED IN DPC MICELLES Solved by: NMR, Identified by HHSEARCH |
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2low: SOLUTION STRUCTURE OF AR55 IN 50% HFIP Solved by: NMR, Identified by HHSEARCH |
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2lov: AR55 SOLUBILISED IN LPPG MICELLES Solved by: NMR, Identified by HHSEARCH |
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1hll: NMR STRUCTURE OF T3-I2, A 32 RESIDUE PEPTIDE FROM THE ALPH2A ADRENERGIC RECEPTOR Solved by: NMR, Identified by HHSEARCH |
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1hof: NMR STRUCTURE OF T3-I2, A 32 RESIDUE PEPTIDE FROM THE ALPH2A ADRENERGIC RECEPTOR Solved by: NMR, Identified by HHSEARCH |
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1hod: NMR STRUCTURE OF D130I MUTANT T3-I2, A 32 RESIDUE PEPTIDE FROM THE ALPHA 2A ADRENERGIC RECEPTOR Solved by: NMR, Identified by HHSEARCH |
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1ho9: BEST 20 NMR CONFORMERS OF D130I MUTANT T3-I2, A 32 RESIDUEPEPTIDE FROM THE ALPHA 2A ADRENERGIC RECEPTOR Solved by: NMR, Identified by HHSEARCH |
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4iar: CRYSTAL STRUCTURE OF THE CHIMERIC PROTEIN OF 5-HT1B-BRIL IWITH ERGOTAMINE (PSI COMMUNITY TARGET, E. XU) Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH |
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4ib4: CRYSTAL STRUCTURE OF THE CHIMERIC PROTEIN OF 5-HT2B-BRIL IWITH ERGOTAMINE Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH |
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4iaq: CRYSTAL STRUCTURE OF THE CHIMERIC PROTEIN OF 5-HT1B-BRIL IWITH DIHYDROERGOTAMINE (PSI COMMUNITY TARGET, E. XU) 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.