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
4gnsB 31 gyqflnrdif kscprimerq fgeclhnrth likdlissgn vglgpieivh
4gnsB hhhhhhhh h ssss hhhhhhhh hhhhhhh ssss
4gnsB 81 msylnkheke efgeyfyvtg ievsgpampv eflevlkssk risknisnni
4gnsB ssssss s sssssssss hhhh hhhhhhhh sss
4gnsB 131 iltyccfnff snldiriryd addtfqttai dcnkettdlt mtekmweetf
4gnsB ssssssss ssssssss sssssss s sss hhhhhhhh
4gnsB 181 assviraiit ntnpelkppg lvecpfyvgk dtissckkii ellcrflprs
4gnsB hhhhhhhhhh hh sss hhhhhhhhh hhhh
4gnsB 231 lncgwdstks mqativnnyl myslksfiai tpslvdftid ylkgltkkdp
4gnsB hh hh hhhhhhhh h hhhhh hhhhhhh
4gnsB 281 ihdiyyktam itildhietk eldmitilne tldpllslln dlpprdadsa
4gnsB hhhhhhh hhhh hhhhhhhhh hhhhhhhhhh hhh
4gnsB 331 rlmncmsdll niqtnfllnr gdyelalgvs ntstelalds feswynlarc
4gnsB hhhhhhhhhh hhhhhhhh hhhhhhhhh hhhhhh hhhhhhhhh
4gnsB 381 hikkeeyeka lfainsmprr fltsnyykkp lngtrehydl tameftnlsg
4gnsB hhhh hhh hhhhh sss hhhhhhhhh
4gnsB 444 tlrnwkedel krqifgriam inekkigytk eiwddiaikl gpicgpqsvn
4gnsB h hhhh hh sssss h hhh hh
4gnsB 494 linyvspqev knikninlia rntigkqlgw fsgkiygllm eivnkigwng
4gnsB hhh h hhhh h hhhhhhhhhh hhhh hhh
TARGET 1 GDRPLLWST
4gnsB 544 llnirteafm mcegwlddlf ldlyqdlkls kislsnkde- -khsglewel
TARGET hhhhhh
4gnsB hhhhhhhhhh hhhhhhh hhhhhhhhhh hhhhhh
TARGET 10 LGQSLMKHGE WQEASLAFRA ALKQRPDAYD YAWLADALDR LH -------
4gnsB 619 lglimlrtwh wedavaclrt sivarfdpvs cqqllkiylq ppkniqevtl
TARGET hhhhhh h hhhhhhhhhh hhh hhh hhhhhhhhh
4gnsB hhhhhh h hhhhhhhhhh hhh hhhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
4gnsB 669 ldtdtiisll ikkisydcry ynycqifnlq lleklcnelg thilrnkill
TARGET
4gnsB hhhhhhhh hhhhhhhh hhhhh hhhhhhhh hhhhhhhh
TARGET ---------- ---------- -----
4gnsB 719 qpsigdeimv midamlawia dldht
TARGET
4gnsB hhhh hhhhhhhhhh hh
Template's ligands section
Ligands in the template:EPE : 1,GOL : 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
4gns is annotated as HETERO TETRAMER
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: 4gns.pdb1.gz
Quaternary Structure Modelling of the Target Protein
4gns_1
Template Selection
- Start SMR-Pipeline for:149fb7a87508140bd49dfb75a2489068 on BC2-cluster at Sat Feb 23 09:12:00
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...
- Generate new template library
- Run template selection against modfied template library
- Summarize templates:
- 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
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:10): model based on new templates
- Send 10 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- **********
- building model based on 4gnsB (325-375) was successful
- *****************
- building model based on 3vtxB (308-393) was successful
- ***************************
- building model based on 3vtxA (263-394) was successful
- **************
- building model based on 3vtxA (84-153) was successful
- ************
- building model based on 3vtxB (155-213) was successful
- ****************************
- building model based on 3vtyD (84-220) was successful
- ************************************************
- building model based on 3vtyA (155-394) was successful
- ******************************************
- building model based on 3vtyD (87-296) was successful
- ********************************************************
- building model based on 4i17A (118-394) was successful
- ********************************************************
- building model based on 3vtxA (84-361) 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:149fb7a87508140bd49dfb75a2489068 on BC2-cluster at Sat Feb 23 09:15:26
2013
Template Search
| Template Description |
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4gns: CRYSTAL STRUCTURE OF THE CHS5-CHS6 EXOMER CARGO ADAPTOR CO Solved by: X-RAY, Resolution: 2.75A, Identified by HHSEARCH |
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3vtx: CRYSTAL STRUCTURE OF MAMA PROTEIN Solved by: X-RAY, Resolution: 1.75A, Identified by HHSEARCH |
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4i17: CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN (BF2334) FROM FRAGILIS NCTC 9343 AT 1.50 A RESOLUTION Solved by: X-RAY, Resolution: 1.83A, Identified by HHSEARCH |
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3vty: CRYSTAL STRUCTURE OF MAMA Solved by: X-RAY, Resolution: 2.00A, 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.