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 STKILSLN TGAQIPQIGL GTWQSKENDA YKAVLTALKD GYRHIDTAAI
3oncA 1 asril-ln ngakmpilgl gtwksppgqv teavkvaidv gyrhidcahv
TARGET sss sss ss s h hhhhhhhhhh sssss
3oncA ssss s sssss ss s h hhhhhhhhhh sssss
TARGET 49 YRNEDQVGQA IK----DSGV PREEIFVTTK LWCTQHHEPE VAL--DQSLK
3oncA 48 yqnenevgva iqeklreqvv kreelfivsk lwctyhekgl vkgacqktls
TARGET hhhhhhh h sssss s hhh
3oncA hhhhhhh hhhhhhh sssss s hhhhhhhhhh
TARGET 93 RLGLDYVDLY LMHWPARLDP AYIKNEDILS VPTKKDGSRA VDITNWNFIK
3oncA 98 dlkldyldly lihwpagfkp g----keffp l----desgn vvpsdtnild
TARGET hh sss sss sss sss hhh
3oncA hh sss sss sss s s s s ssss hhh
TARGET 143 TWELMQELPK TGKTKAVGVS NFSINNLKDL LASQGNKLTP AANQVEIHPL
3oncA 140 twaameelvd eglvkaigis nfnhlqvemi lnkpglkykp avnqiechpy
TARGET hhhhhhhhhh h sssss s hhhhhhh hh sssssss
3oncA hhhhhhhhhh h sssss s hhhhhhh hh sssssss
TARGET 193 LPQDELINFC KSKGIVVEAY SPLGST---- ----DAPLLK EPVILEIAKK
3oncA 190 ltqekliqyc qskgivvtay splgspdrpw akpedpslle dprikaiaak
TARGET hhhhhhh hhh sssss hhhhhhhhh
3oncA hhhhhhh hhh sssss hhhhhhhhh
TARGET 235 NNVQPGHVVI SWHVQRGYVV LPKSVNPDRI KTNRKI--FT LSTEDFEAI
3oncA 240 hnkttaqvli rfpmqrnlvv ipksvtperi aenfkvfdfe lssqdmttll
TARGET h hhhhhh hhhh s ss hhhh hhh hhhhhhh
3oncA h hhhhhh hhhhh s ss hhhh hhh hhhhhhhh
TARGET ---------- ---------- ---
3oncA 290 synrnwrvca llsctshkdy pfh
TARGET
3oncA h
Template's ligands section
Ligands in the template:BR : 1,CIT : 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
3onc 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: 3onc.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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.254 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:6b6151388260f4a072d2f96d4f639b19 on BC2-cluster at Mon Feb 18 15:35:47
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 D found
- No template with F found
- No template with C found
- No template with E found
- No template with E found
- No template with D found
- No template with A found
- No template with B found
- No template with C found
- No template with E found
- No template with F found
- No template with G found
- No template with H found
- No template with A found
- No template with B found
- No template with C found
- No template with D found
- No template with F found
- No template with G found
- No template with H found
- No template with A found
- No template with G found
- No template with H 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 3oncA (8-288) was successful
- ****************************************************************************
- building model based on 2he8A (14-308) 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:6b6151388260f4a072d2f96d4f639b19 on BC2-cluster at Mon Feb 18 15:38:37
2013
Template Search
| Template Description |
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4exa: CRYSTAL STRUCTURE OF THE PA4992, THE PUTATIVE ALDO-KETO REPSEUDOMONA AERUGINOSA Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH |
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4exb: PUTATIVE ALDO-KETO REDUCTASE FROM PSEUDOMONA AERUGINOSA Solved by: X-RAY, Resolution: 2.75A, 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.