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 VKVMTWNVNG LRGLLKFESF SALQLAQREN
3u8u_3#2 44 lyedppdqkt spsgkpat-- lkicswnvdg lrawikkk-- -gldwvkeea
TARGET ssssssss hhhhh hhhhhh
3u8u_3#2 ss s sss ssssssss hhhhh hhhhhhhh
TARGET 31 FDILCLQETK LQ-VKDVEEI KKTLIDGYDH SFWSCSVSKL GYSGTAIISR
3u8u_3#2 89 pdilclqetk csenklpael qe--lpglsh qywsapsdke gysgvgllsr
TARGET ssssssss hh s ssss ssssssss
3u8u_3#2 ssssssss hh h s ssss ssssssss
TARGET 80 IKPLSVRYGT GLSGHDTEGR IVTAEFDSFY LINTYVPNSG DGLKRLSYRI
3u8u_3#2 137 qcplkvsygi gdeehdqegr vivaefdsfv lvtayvpnag rglvrleyr-
TARGET sssss s ssssss ss ssssss ss s sss
3u8u_3#2 sssss s ssssss ss ssssss hhhh
TARGET 130 EEWDRTLSNH IKELEKSKPV VLTGDLNCAH EEIDIFNPAG NKRSAGFTIE
3u8u_3#2 186 qrwdeafrkf lkglasrkpl vlcgdlnvah eeidlrnpkg nkknagftpq
TARGET hhhhhhhhhh hhhhhhh ss ssssss sss hh
3u8u_3#2 hhhhhhhhhh hhhhhhh ss ssssss sss hh
TARGET 180 ERQSFGANLL DKGFVDTFRK QHPGVV-GYT YWGYRHGGRK TNKGWRLDYF
3u8u_3#2 236 erqgfgellq avpladsfrh lypntpyayt fwtymmnars knvgwrldyf
TARGET hhhhhhhhhh h ssshhh h s ss hhh h sssssss
3u8u_3#2 hhhhhhhhhh h ssshhh h s ss hhh h sssssss
TARGET 229 LVSQSIAANV HDSYILPDIN GSDHCPIGLI LKL
3u8u_3#2 286 llshsllpal cdskirskal gsdhcpitly lal-
TARGET sss hss ssssss ssssssss ss
3u8u_3#2 sss hss ssssss ssssssss ss
Template's ligands section
Ligands in the template:CL : 1,MG : 1.
Ligands in the template that will be assessed: MG1.
Model's ligands section
MG1
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand z.MG1 will not be included in the final model.
MG1: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3u8u 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: 3u8u.pdb3.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template can be assumed to be similar (=MONOMER)
The corresponding reliability score is 0.588 (>0.5 indicates similarity)
Model was succesfully built as MONOMER.
Template Selection
- Start SMR-Pipeline for:a872d702f3a5c3777e50af0347cd2ce7 on BC2-cluster at Tue Feb 19 07:26:40
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:
- 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 3u8uC (276-536) was successful
- ********************************************
- building model based on 2j63B (241-535) 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:a872d702f3a5c3777e50af0347cd2ce7 on BC2-cluster at Tue Feb 19 07:29:50
2013
Template Search
| Template Description |
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4fva: CRYSTAL STRUCTURE OF TRUNCATED CAENORHABDITIS ELEGANS TDP2 Solved by: X-RAY, Resolution: 2.07A, Identified by HHSEARCH |
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4gew: CRYSTAL STRUCTURE OF TDP2 FROM C. ELEGANS Solved by: X-RAY, Resolution: 2.35A, Identified by HHSEARCH |
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4f1i: CRYSTAL STRUCTURE OF SEMET TDP2 FROM CAENORHABDITIS ELEGAN Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH |
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4f1h: CRYSTAL STRUCTURE OF TDP2 FROM DANIO RERIO COMPLEXED WITH STRAND DNA Solved by: X-RAY, Resolution: 1.66A, Identified by HHSEARCH |
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4fpv: CRYSTAL STRUCTURE OF D. RERIO TDP2 COMPLEXED WITH SINGLE SPRODUCT Solved by: X-RAY, Resolution: 1.73A, Identified by HHSEARCH |
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4gyz: MUS MUSCULUS TDP2 BOUND TO DAMP AND MG2+ Solved by: X-RAY, Resolution: 2.56A, Identified by HHSEARCH |
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4gz2: MUS MUSCULUS TDP2 EXCLUDED SSDNA COMPLEX Solved by: X-RAY, Resolution: 1.85A, Identified by HHSEARCH |
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4gz1: MUS MUSCULUS TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)COMPLEX AT 1.5 ANGSTROMS RESOLUTION Solved by: X-RAY, Resolution: 1.50A, Identified by HHSEARCH |
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4gz0: MUS MUSCULUS TDP2-DNA SUBSTRATE ANALOG (5'-6-AMINOHEXANOL) Solved by: X-RAY, Resolution: 2.11A, 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.