SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | Q24432 |
Database: TrEMBL (Unreviewed)  |
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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 DPKVTLEG KDLWEKFHKL GTEMVITKSG RQMFPQMKFR VSGLDAKAKY
1h6f_1#3 102 dpkvhlea kelwdqfhkr gtemvitksg rrmfppfkvr csgldkkaky
TARGET sssss hhhhhhhhhh sssss sss ss sss
1h6f_1#3 sssss hhhhhhhhhh sssss sss ss sss
TARGET 49 ILLLDIVAAD DYRYKFHNSR WMVAGKADPE MPKRMYIHPD SPTTGEQWMQ
1h6f_1#3 150 illmdiiaad dcrykfhnsr wmvagkadpe mpkrmyihpd spatgeqwms
TARGET sssssssss sssssss s sssssss sss ssshhh
1h6f_1#3 sssssssss sssssss s sssssss sss ssshhh
TARGET 99 KVVSFHKLKL TNNISDKHGF VSTTILNSMH KYQPRFHLVR ANDILKLPYS
1h6f_1#3 200 kvvtfhklkl tnnisdkhgf ---tilnsmh kyqprfhivr andilklpys
TARGET ss s sss s ssssssssss s hhh
1h6f_1#3 ss s sss s ssssssssss s
TARGET 149 TFRTYVFKET EFIAVTAYQN EKITQLKIDN NPFAKGFRD -- DDPKVTL
1h6f_1#3 247 tfrtylfpet efiavtayqn dkitqlkidn npfakgfrd- k--ddpkvhl
*
TARGET sss ssss hhhhhhhhh h ssss
1h6f_1#3 sss ssss hhhhhhhhh h ssss
TARGET 195 EGKDLWEKFH KLGTEMVITK SGRQMFPQMK FRVSGLDAKA KYILLLDIVA
1h6f_1#3 108 eakelwdqfh krgtemvitk sgrrmfppfk vrcsgldkka kyillmdiia
TARGET s hhhhhhhh hh sssss ss ssss s ssssssssss
1h6f_1#3 s hhhhhhhh hh sssss s ssss s ssssssssss
TARGET 245 ADDYRYKFHN SRWMVAGKAD PEMPKRMYIH PDSPTTGEQW MQKVVSFHKL
1h6f_1#3 158 addcrykfhn srwmvagkad pempkrmyih pdspatgeqw mskvvtfhkl
TARGET s sssssss ssssssss sss ssshhh h sss
1h6f_1#3 s sssssss ssssssss sss ssshhh h
TARGET 295 KLTNNISDKH GFVSTTILNS MHKYQPRFHL VRANDILKLP YSTFRTYVFK
1h6f_1#3 208 kltnnisdkh gf---tilns mhkyqprfhi vrandilklp ystfrtylfp
TARGET sssssssss sss sss
1h6f_1#3 sss sss sssssssss sss sss
TARGET 345 ETEFIAVTAY QNEKITQLKI DNNPFAKGFR D
1h6f_1#3 255 etefiavtay qndkitqlki dnnpfakgfr d-
TARGET ssss hhhhhhhh h
1h6f_1#3 ssss hhhhhhhh h h
Template's ligands section
Ligands in the template:DA : 16,DC : 8,DG : 8,DT : 16,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
1h6f is annotated as 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: 1h6f.pdb1.gz
Quaternary Structure Modelling of the Target Protein
The quaternary structure can be assumed to be identical
To build the complex the following chains of the complex has been additionally identified: 1h6fA
Model was succesfully built as DIMER.
Template Selection
- Start SMR-Pipeline for:5971df2d070e14042c68f0a1686720c2 on BC2-cluster at Thu Feb 21 09:33:24
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 1
- But still uncovered regions of the target sequence detected, go for: HHSEARCH
FATAL - No A3m found
- Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
- Warning: Oligomer Prediction was not successfull!
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:1): model based on new templates
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ***************
- building model based on 1h6fB (326-513) 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:5971df2d070e14042c68f0a1686720c2 on BC2-cluster at Thu Feb 21 09:35:16
2013
Template Search
| Template Description |
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1h6f: HUMAN TBX3, A TRANSCRIPTION FACTOR RESPONSIBLE FOR ULNAR- MAMMARY SYNDROME, BOUND TO A PALINDROMIC DNA SITE Solved by: X-RAY, Resolution: 1.70A, Identified by BLAST |
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2x6v: CRYSTAL STRUCTURE OF HUMAN TBX5 IN THE DNA-BOUND AND DNA- FREE FORM Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST |
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2x6u: CRYSTAL STRUCTURE OF HUMAN TBX5 IN THE DNA-FREE FORM Solved by: X-RAY, Resolution: 1.90A, 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.