SWISS-MODEL Repository 
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
Domain
Model 3D Structure
|
|
|
|
|||||||||||||||||||||||||||||||
|
Template Links:
[ RCSB ]
[ PDBe ]
[ SCOP ]
[ CATH ]
display model: in [ AstexViewer ] download model: as [ pdb ] - as [ Deepview project ] |
Alignment
TARGET 1 SLYLWID AHQARVLIGF EEDILIVSEG KMAPFTHDFR KAQQRMPAIP
2ygqA 34 g--slylwid ahqarvligf eedilivseg kmapfthdfr kaqqrmpaip
TARGET ssssss hhhhhhh ssssss sss hh h hhhh
2ygqA sssss hhhhhhh ssssss sss hh h hhhh
TARGET 48 VNIHSMNFTW QAAGQAEYFY EFLSLRSLDK GIMADPTVNV PLLGTVPHKA
2ygqA 82 vnihsmnftw qaagqaeyfy eflslrsldk gimadptvnv pllgtvphka
TARGET sssssss sss sss ssssssss sss sss sssss
2ygqA sssssss s sss ssssssss sss sss sssss
TARGET 98 SVVQVGFPCL GKQDGVAAFE VDVIVMNSEG NTILQTPQNA IFFKTCQQAE
2ygqA 132 svvqvgfpcl gkqdgvaafe vdvivmnseg ntilktpqna iffktcqqae
TARGET ssssssssss ssssss sssssss ssssss sssss
2ygqA ssssssssss ssssss sssssss ssssss sssss
TARGET 148 CPGGCRNGGF CNERRICECP DGFHGPHCEK ALCTPRCMNG GLCVTPGFCI
2ygqA 182 cpggcrnggf cnerricecp dgfhgphcek alctprcmng glcvtpgfci
TARGET s ss sss
2ygqA s ss sss
TARGET 198 CPPGFYGVNC DKANCSTTCF NGGTCFYPGK CICPPGLEGE QCE
2ygqA 232 cppgfygvnc dkancsttcf nggtcfypgk cicppglege qce-
TARGET
2ygqA
Template's ligands section
Ligands in the template:FUC : 1,SCR : 1.
Ligands in the template that will be assessed: FUC1278.
Model's ligands section
FUC1278
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand A.FUC1278 will not be included in the model.
FUC1278: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2ygq is annotated as TRIMER
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: 2ygq.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 (=TRIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.044 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:90221bc2ed7720ccc156660a00d044b9 on BC2-cluster at Thu Apr 4 11:08:45
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
FATAL - 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 C found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with G found
- No template with C found
- No template with E found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with A found
- No template with C found
- No template with H found
- No template with H found
- No template with H found
- No template with H found
- No template with A found
- No template with A found
- No template with E found
- No template with A found
- No template with G found
- No template with C found
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:6): model based on new templates
- Send 6 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ***************************************************
- building model based on 2ygqA (35-274) was successful
- *************
- building model based on 3ho3A (244-305) was not successful go to next best template
- *************
- building model based on 3ho5B (244-305) was not successful go to next best template
- *************
- building model based on 3ho5A (244-305) was not successful go to next best template
- *************
- building model based on 3ho4B (244-305) was not successful go to next best template
- *************
- building model based on 3ho4A (244-305) was not successful go to next best template
- *************
- building model based on 2wg4B (244-305) was not successful go to next best template
- **************
- building model based on 2wftA (244-307) was successful
- **************
- building model based on 2wfxB (264-331) was successful
- ********************
- building model based on 2ygqA (241-337) was successful
- ************************
- building model based on 2vj2A (192-305) was successful
- ****************************
- building model based on 2gy5A (206-339) 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:90221bc2ed7720ccc156660a00d044b9 on BC2-cluster at Thu Apr 4 11:11:36
2013
Template Search
| Template Description |
|
||||||||||||||||||||
|
2ygq: WIF DOMAIN-EPIDERMAL GROWTH FACTOR (EGF)-LIKE DOMAINS 1-3 WNT INHIBITORY FACTOR 1 IN COMPLEX WITH 1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE Solved by: X-RAY, Resolution: 3.95A, Identified by BLAST |
|
||||||||||||||||||||
|
2d3j: NMR STRUCTURE OF THE WIF DOMAIN FROM HUMAN WIF-1 Solved by: NMR, Identified by BLAST |
|
||||||||||||||||||||
|
2ygo: WIF DOMAIN-EGF-LIKE DOMAIN 1 OF HUMAN WNT INHIBITORY FACTO1 IN COMPLEX WITH 1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE Solved by: X-RAY, Resolution: 1.85A, Identified by BLAST |
|
||||||||||||||||||||
|
2ygn: WIF DOMAIN OF HUMAN WNT INHIBITORY FACTOR 1 IN COMPLEX WIT1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE Solved by: X-RAY, Resolution: 1.85A, Identified by BLAST |
|
||||||||||||||||||||
|
2ygp: WIF DOMAIN-EGF-LIKE DOMAIN 1 MET77TRP OF HUMAN WNT INHIBIT1 IN COMPLEX WITH 1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE Solved by: X-RAY, Resolution: 2.22A, Identified by BLAST |
|
||||||||||||||||||||
|
4bdx: THE STUCTURE OF THE FNI-EGF TANDEM DOMAIN OF COAGULATION F Solved by: X-RAY, Resolution: 1.62A, Identified by HHSEARCH |
|
||||||||||||||||||||
|
4bdw: THE STUCTURE OF THE FNI-EGF TANDEM DOMAIN OF COAGULATION FIN COMPLEX WITH HOLMIUM Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH |
|
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.