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 YDPLHIYI SQYLKQLRSK YTFEKDISIF AGTFNISGKI PKDDIKDWIF
1i9zA 534 ydpiheyv nhelrkrene fsehknvkif vasynlngcs attklenwlf
TARGET hhhhhh hhhhh ssssssssss ssssss hhhh
1i9zA hhhhhh hhhhh ssssssssss ssssss hhhh
TARGET 49 PKSMSKEDEM ADLYVIGLEE VVELTPGHML ATDPYVRQFW EKKILTLLNG
1i9zA 582 pentp----l adiyvvgfqe ivqlt----- sadpakrrew escvkrllng
TARGET sssssssss hhhhhh hhhhhhhhhh
1i9zA sssssssss hhhhhhh hhhhhhhhhh
TARGET 99 P-----GRKK KYIRLWSTQL GGILLLLFMN ETEYSKVKHI EGDVKKTGFG
1i9zA 628 kctsgpg--- -yvqlrsgql vgtalmifck esclpsiknv egtvkktglg
TARGET ssssssss sssssssss hhhhsss sssssss
1i9zA s sssssssss sssssssss shhhhsss sssssss
TARGET 144 GMASNKGAVA VSFKYSATRF CVLVSHLAAG LENVEQRHND YKTIAKSIRF
1i9zA 678 ----nkgava irfdyedtgl cfitshlaag ytnyderdhd yrtiasglrf
TARGET sssss ssssss sss sssssss hhhhhh hhhhhhh
1i9zA sssss ssssss sss sssssss hhhhhhh hhhhhhh
TARGET 194 SKGLRIKDHD AIIWMGDFNY RILMSNEDVR RKIVSKEYAS LFEKDQLNQQ
1i9zA 724 rrgrsifnhd yvvwfgdfny risltyeevv pciaqgklsy lfeydqlnkq
TARGET ssssssss sss hhhhh hhh hhhh hh ssshhhh
1i9zA ssssssss hhhhh hhh hhhh hh hhhhh
TARGET 244 MIAGESFPYF HEMAIDFPPT YKFDPGTKNY DTSEKMRIPA WTDRILSRGE
1i9zA 774 mltgkvfpff selpitfppt ykfdigtdiy dtsdkhrvpa wtdrilyrge
TARGET hh s ssss ss s sssssss
1i9zA hh sss ss s sssssss
TARGET 294 VLEQLEYKCC EDILFSDHRP VYAIFRARVT VVDEQKKTTL GTQIYEK --
1i9zA 824 lvph-syqsv p-lyysdhrp iyatyeaniv kvdrekkkil feelynqrkq
TARGET sss sss ssss ssssssssss ssshhhhhhh hhhhhhh
1i9zA sss sssss s ssssssssss ssshhhhhhh hhhhhhhhhh
TARGET -------
1i9zA 872 evrdasq
TARGET
1i9zA hhhhh
Template's ligands section
Ligands in the template:2IP : 1,CA : 1.
Ligands in the template that will be assessed: CA301.
Model's ligands section
CA301
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand CA301 will not be included in the final model.
CA301: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
1i9z 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: 1i9z.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 0.446 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:6d10f710b26e51fb271525cda25fc064 on BC2-cluster at Mon Feb 18 20:19:04
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 A found
- No template with B 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 1i9zA (503-842) was successful
- *********************************
- building model based on 3lwtX (82-470) was not successful go to next best template
- 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:6d10f710b26e51fb271525cda25fc064 on BC2-cluster at Mon Feb 18 20:23:05
2013
Template Search
| Template Description |
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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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4gz0: MUS MUSCULUS TDP2-DNA SUBSTRATE ANALOG (5'-6-AMINOHEXANOL) Solved by: X-RAY, Resolution: 2.11A, Identified by HHSEARCH |
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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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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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4gew: CRYSTAL STRUCTURE OF TDP2 FROM C. ELEGANS Solved by: X-RAY, Resolution: 2.35A, 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: 2.56A, 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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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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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.