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 YFF NAKLKSDNQE RPKLPITVRR EQVFLDSYRA LFFKTNDEIK
3g1nB 3996 grenl--yfq glerldeglr kedmavhvrr dhvfedsyre lhrkspeemk
TARGET hh hhhhhh sssss hhhhhhhh hhhhh
3g1nB hhh hhh hhhhhh sssssss hhhhhhhh hhhh
TARGET 44 NSKLEITFKG ESGVDAGGVT REWYQVLSRQ MFNPDYALFL PVPSDKTTFH
3g1nB 4044 n-rlyivfeg eegqdaggll rewymiisre mfnpmyalfr tspgdrvtyt
TARGET sssss hhhhh hhhhhhhhhh sss ss sss
3g1nB sssssss hhhhh hhhhhhhhhh h sss ss sss
TARGET 94 PNRTSGINPE HLSFFKFIGM IIGKAIRDQC FLDCHFSREV YKNILGRPVS
3g1nB 4093 inpsshcnpn hlsyfkfvgr ivakavydnr llecyftrsf ykhilgksvr
TARGET ss hhh hhhhhhhhhh hhhhhhhh hh hhhhh
3g1nB ss hhh hhhhhhhhhh hhhhhhhh hh hhhhh
TARGET 144 LKDMESLDPD YYKSLVWILE NDITDI-IEE TFSVETDDYG EHKVINLIEG
3g1nB 4143 ytdmesedyh fyqglvylle ndvstlgydl tfstevqefg vcevrdlkpn
TARGET hhhhh h hhhhhhhhhh s ssssssss sssssss
3g1nB hh h hhhhhhhhhh hh s ssssssss sssssss
TARGET 193 GKDIIVTEAN KQDYVKKVVE YKLQTSVKEQ MDNFLVGFYA LISKDLITIF
3g1nB 4193 ganilvteen kkeyvhlvcq mrmtgairkq laaflegfye iipkrlisif
TARGET sss hhhhhhhhhh hhh hhh hhhhhhhhh hhhh
3g1nB sss hhhhhhhhhh hhh hhh hhhhhhhhh hhhh
TARGET 243 DEQELELLIS GLPDIDVDDW KNNTTYVNYT ATCKEVSYFW RAVRSFDAEE
3g1nB 4243 teqelellis glptididdl ksnteyhkyq snsiqiqwfw ralrsfdqad
TARGET hhhhhhhh hhhh hh sss hhhhhhh hhh hhhh
3g1nB hhhhhhhhh hhhh hh sss hhhh hhh hhhh
TARGET 293 RAKLLQFVTG TSKVPLNGFK ELSGVNGVCK FSIHRDFGSS ERLPSSHTCF
3g1nB 4293 rakflqfvtg tskvplqgfa alegmngiqk fqihrddrst drlpsahtcf
TARGET hhhhhhhh sss sss ssssss ssss
3g1nB hhhhhhhh sss sss ssssss ssss
TARGET 343 NQLNLPPYES YETLRGSLLL AINE
3g1nB 4343 nqldlpayes feklrhmlll aiqe-
TARGET sssss hhhhhhhhhh h
3g1nB sssss hhhhhhhhhh h
Template's ligands section
Ligands in the template:NA : 1.
Ligands in the template that will be assessed: NA5002.
Model's ligands section
NA5002
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.080
Given the properties calculated previously, the ligand B.NA5002 will be included in the final model.
NA5002: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
3g1n is annotated as MONOMER
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: 3g1n.pdb2.gz
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 52.044) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode
The target structure was calculated as SINGLE CHAIN
Template Selection
- Start SMR-Pipeline for:3d19ffaf60b1c6883a1abf65b964975f on BC2-cluster at Mon Feb 18 22:13:47
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- 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 B found
- No template with B found
- No template with D found
- No template with A found
- No template with X found
- No template with B found
- No template with Y found
- No template with D found
- No template with C found
- No template with C found
- No template with C found
- No template with C found
- No template with C found
- No template with C found
- No template with C found
- No template with A found
- No template with X found
- No template with B found
- No template with Y found
- Warning: Oligomer Prediction was not successfull!
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:7): model based on new templates
- Send 7 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *********
- building model based on 3g1nB (2895-3260) was successful
- *
- building model based on 4b8pB (601-636) was successful
- *
- building model based on 4b8pB (419-478) was successful
- ****
- building model based on 4b8pB (323-480) was not successful go to next best template
- ****
- building model based on 4b8pA (323-480) was not successful go to next best template
- ****
- building model based on 2ynsB (323-478) was successful
- ***
- building model based on 4b8pB (532-639) was successful
- ********
- building model based on 4b8jA (297-641) was successful
- ***********
- building model based on 4b8jA (324-770) was not successful go to next best template
- ***********
- building model based on 2ynsB (326-770) was not successful go to next best template
- ***********
- building model based on 2ynsA (326-770) was not successful go to next best template
- ***********
- building model based on 4b8oA (326-770) was not successful go to next best template
- ***********
- building model based on 4b8pB (327-770) 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:3d19ffaf60b1c6883a1abf65b964975f on BC2-cluster at Mon Feb 18 22:27:07
2013
Template Search
| Template Description |
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4hxt: CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTUCONSORTIUM TARGET OR329 Solved by: X-RAY, Resolution: 1.95A, Identified by HHSEARCH |
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4b8j: RIMP_ALPHA1A Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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4b8p: RIMP_ALPHA_A89NLS Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH |
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2yns: RIMP_ALPHA_B54NLS Solved by: X-RAY, Resolution: 2.08A, Identified by HHSEARCH |
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4b8o: RIMP_ALPHA_SV40TAGNLS Solved by: X-RAY, Resolution: 2.08A, 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.