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 ] 
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 MAVQPKET LQLEGAAEAG FVRFFEGMPE KPSTTVRLFD RGDFYTAHGE
2o8bA 1 mavqpket lqlesaaevg fvrffqgmpe kptttvrlfd rgdfytahge
TARGET hhhhhh hhhhhh sssssss s ssssssh
2o8bA hhhhhh hhhhhh sssssss s ssssssh
TARGET 49 DALLAAREVF KTQGVIKYMG PAGSKTLQSV VLSKMNFESF VKDLLLVRQY
2o8bA 49 dallaarevf ktqgvikymg pagaknlqsv vlskmnfesf vkdlllvrqy
TARGET hhhhhhhhh sss ssss ss hhhhhhh hhhhhh
2o8bA hhhhhhhhh ssss s sssssss ss hhhhhhh hhhhhh
TARGET 99 RVEVYKNKAG NKASKENEWY LAFKASPGNL SQFEDILFGN NDMSASVGVM
2o8bA 99 rvevyknrag ---skendwy laykaspgnl sqfedilfgn n-----igvv
TARGET ssssssss sss sssss hhhh sss
2o8bA ssssssss sss sssss hhhh sss
TARGET 149 GIKMAVVDGQ RHVGVGYVDS TQRKLGLCEF PENDQFSNLE ALLIQIGPKE
2o8bA 149 gvkmsavdgq rqvgvgyvds iqrklglcef pdndqfsnle alliqigpke
TARGET sssss sssssssss ssssssss hhh hhhhhh ss
2o8bA sssss sssssssss ssssssss hhh hhhhhh ss
TARGET 199 CVLPGGETTG DMGKLRQVIQ RGGILITERK RADFSTKDIY QDLNRLLKGK
2o8bA 199 cvlpggetag dmgklrqiiq rggiliterk kadfstkdiy qdlnr---gk
TARGET sss hhhhhhhh sssss hh h sss
2o8bA sss hhhhhhhh sssss hh h
TARGET 249 KGEQINSAAL PEMENQVAVS SLSAVIKFLE LLSDDSNFGQ FELATFDFSQ
2o8bA 249 kgeqmnsavl pemenqvavs slsavikfle llsddsnfgq felttfdfsq
TARGET hh h hhhhh hhhhhhhh ss s
2o8bA hh hhhhhh hhhhhhhh
TARGET 299 YMKLDMAAVR ALNLFQGSVE DTTGSQSLAA LLNKCKTAQG QRLVNQWIKQ
2o8bA 299 ymkldiaavr alnlfqgs-- --tgsqslaa llnkcktpqg qrlvnqwikq
TARGET hhhhh hh hhh hh hhh hhhhhhhhh
2o8bA hhhhh hh hhh hh hhh hhhhhhhhh
TARGET 349 PLMDRNRIEE RLNLVEAFVE DSELRQSLQE DLLRRFPDLN RLAKKFQRQA
2o8bA 349 plmdknriee rlnlveafve daelrqtlqe dllrrfpdln rlakkfqrqa
TARGET hhhhhh hhhhhhhhhh hhhhhh h hhhhhhhh
2o8bA hhhhhh hhhhhhhhhh hhhhhh hh h hhhhhhh
TARGET 399 ANLQDCYRLY QGINQLPSVI QALEKYEGRH QALLLAVFVT PLIDLRSDFS
2o8bA 399 anlqdcyrly qginqlpnvi qalekhegkh qklllavfvt pltdlrsdfs
TARGET hhhhhhh hhh hhhh hhhh h hhhhhhh
2o8bA hhhhhhh hhh hhhh hhhh h hhhhhhh
TARGET 449 KFQEMIETTL DMDQVENHEF LVKPSFDPNL SELREVMDGL EKKMQSTLIN
2o8bA 449 kfqemiettl dmdqvenhef lvkpsfdpnl selreimndl ekkmqstlis
TARGET hhhhhhhh hhhh hhh hhhhhhhhhh hhhhhhhhhh
2o8bA hhhhhhhh hhhh hhh hhhhhhhhhh hhhhhhhhhh
TARGET 499 AARGLGLDPG KQIKLDSSAQ FGYYFRVTCK EEKVLRNNKN FSTVDIQKNG
2o8bA 499 aardlgldpg kqikldssaq fgyyfrvtck eekvlrnnkn fstvdiqkng
TARGET hhhh sssss ssssss ssssss s
2o8bA hhhh sssss ssssss ssssss s
TARGET 549 VKFTNSELSS LNEEYTKNKG EYEEAQDAIV KEIVNISSGY VEPMQTLNDV
2o8bA 549 vkftnsklts lneeytknkt eyeeaqdaiv keivnissgy vepmqtlndv
TARGET ssss hhhh hh hhhhh hhhhhhhhhh hhhhhh h hhhhhhhhhh
2o8bA ssss hhhh hh hhhhh hhhhhhhhhh hhhhhhhh hhhhhh
TARGET 599 LAHLDAIVSF AHVSNAAPVP YVRPVILEKG KGRIILKASR HACVEVQDEV
2o8bA 599 laqldavvsf ahvsngapvp yvrpailekg qgriilkasr hacvevqdei
TARGET hhhhhhhhhh hhhhh sss sssss hhhhh
2o8bA hhhhhhhhhh hhhhh sss sssss hhhhh
TARGET 649 AFIPNDVHFE KDKQMFHIIT GPNMGGKSTY IRQTGVIVLM AQIGCFVPCE
2o8bA 649 afipndvyfe kdkqmfhiit gpnmggksty irqtgvivlm aqigcfvpce
TARGET sss ssssss hhhh hhhhhhhhhh hh
2o8bA sss ssssss hhhh hhhhhhhhhh hh
TARGET 699 SAEVSIVDCI LARVGAGDSQ LKGVSTFMAE MLETASILRS ATKDSLIIID
2o8bA 699 saevsivdci larvg----- ----stfmae mletasilrs atkdsliiid
TARGET sssss ss sss hhhh hhhhhhhh ssssss
2o8bA sssss ss sss hhhh hhhhhhhhh ssssss
TARGET 749 ELGRGTSTYD GFGLAWAISD YIATKIGAFC MFATHFHELT ALANQIPTVN
2o8bA 749 elgrgtstyd gfglawaise yiatkigafc mfathfhelt alanqiptvn
TARGET s hhh hhhhhhhhhh hhhh ss ssss h hhh s
2o8bA s hhh hhhhhhhhhh hhhh ss ssss h hhhhh s
TARGET 799 NLHVTALTTE ETLTMLYQVK KGVCDQSFGI HVAELANFPR HVIACAKQKA
2o8bA 799 nlhvtaltte etltmlyqvk kgvcdqsfgi hvaelanfpk hviecakqka
TARGET ssss s ss hh hhhhhh h hhhhhhhhhh
2o8bA ssss s ss hh hhhhh h hhhhhhhhhh
TARGET 849 LELEEF
2o8bA 849 leleef-
TARGET h
2o8bA h
Template's ligands section
Ligands in the template:ADP : 1,MG : 1.
Ligands in the template that will be assessed: ADP201, MG101.
Model's ligands section
ADP201
ADP201 interacts, within a radius of 3 Angstroem, with the following ions: MG101. They will be considered as a single ligand.
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: 0.030
Given the properties calculated previously, the ligand ADP201 will be included in the model.
ADP201: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
2o8b is annotated as HETERO DIMER
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: 2o8b.pdb1.gz
Quaternary Structure Modelling of the Target Protein
2o8b_1
Template Selection
- Start SMR-Pipeline for:10fcfb595b44f12a53426d314c179e58 on BC2-cluster at Fri Feb 22 16:24:03
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 2 go for
modeling ...
- 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 B found
- No template with B found
- No template with B found
- Warning: Oligomer Prediction was not successfull!
- 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 2o8bA (1-854) was successful
- *******************************************************************************
- building model based on 3thwA (11-930) 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:10fcfb595b44f12a53426d314c179e58 on BC2-cluster at Fri Feb 22 16:35:12
2013
Template Search
| Template Description |
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2o8f: HUMAN MUTSALPHA (MSH2/MSH6) BOUND TO DNA WITH A SINGLE BAST INSERT Solved by: X-RAY, Resolution: 3.25A, Identified by BLAST |
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2o8b: HUMAN MUTSALPHA (MSH2/MSH6) BOUND TO ADP AND A G T MISPAIR Solved by: X-RAY, Resolution: 2.75A, Identified by BLAST |
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2o8d: HUMAN MUTSALPHA (MSH2/MSH6) BOUND TO ADP AND A G DU MISPAI Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST |
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2o8e: HUMAN MUTSALPHA (MSH2/MSH6) BOUND TO A G T MISPAIR, WITH ADP BOUND TO MSH2 ONLY Solved by: X-RAY, Resolution: 3.30A, Identified by BLAST |
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2o8c: HUMAN MUTSALPHA (MSH2/MSH6) BOUND TO ADP AND AN O6-METHYL-GUANINE T MISPAIR Solved by: X-RAY, Resolution: 3.37A, Identified by BLAST |
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3thw: HUMAN MUTSBETA COMPLEXED WITH AN IDL OF 4 BASES (LOOP4) AN Solved by: X-RAY, Resolution: 3.09A, Identified by BLAST |
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3thz: HUMAN MUTSBETA COMPLEXED WITH AN IDL OF 6 BASES (LOOP6) AN Solved by: X-RAY, Resolution: 4.30A, Identified by BLAST |
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3thy: HUMAN MUTSBETA COMPLEXED WITH AN IDL OF 2 BASES (LOOP2) AN Solved by: X-RAY, Resolution: 2.89A, Identified by BLAST |
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3thx: HUMAN MUTSBETA COMPLEXED WITH AN IDL OF 3 BASES (LOOP3) AN Solved by: X-RAY, Resolution: 2.70A, Identified by BLAST |
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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.