SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | O81893 |
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 V GYALTSKKKK SFLQPKLELL ARRKGIFFVA
2q7d_1#8 65529 kihhhhhhmq tflkgkr--v gywlsekkik klnfqafael crkrgmevvq
TARGET s sss hhhhh h hhhhhh hhh ssss
2q7d_1#8 hhhh hh ss s sss hhhhh h hhhhhh hhh ssss
TARGET 32 IDLNRPLSEQ GPFDVVLHKL LGKEW----- ----EEVIED YQ---QKHPE
2q7d_1#8 41 lnlsrpieeq gpldviihkl tdvileadqn dsqslelvhr fqeyidahpe
TARGET s hhh ssssss hhhhh h
2q7d_1#8 s hhh ssssss hhhhhhhh hhhhhhhhh hhhhhhh
TARGET 70 VTVLDPPGSI QRIYNRQSML QGMADLKLSD CSGSLFVPKQ MVVLKDSAAS
2q7d_1#8 91 tivldplpai rtlldrsksy elirkieaym eddricsppf meltslcgdd
TARGET sss hhhh h hhhhhh hhhhhhhhhh ss sss h
2q7d_1#8 sss hhhh h hhhhhh hhhhhhhhhh ss sss h
TARGET 120 ADAVVE-AGL KFPLVAKPLW IDGTAKSHQL YLAYDRRSLA ELDPPLVLQE
2q7d_1#8 141 tmrllekngl tfpficktrv ahgt-nshem aivfnqegln a--ppcvvqn
TARGET hhhhh sssss sss sss sssss
2q7d_1#8 hhhhhhhh sssss sss sss sssss
TARGET 169 FVNHGGVMFK VFVVGDVIKV MRRFSLPNVS NCEKAKVDGV FQFPRVSSAA
2q7d_1#8 190 finhnavlyk vfvvgesytv vqrpslknfs dresi----f fnshnvskpe
TARGET s sss sssss ssss sss sss
2q7d_1#8 s sss sssss ssss sss s s ssshh
TARGET 219 ASADNADLDP RV--AELPPK PFLEALVKEL RSLLGLRLFN IDMIREHGSK
2q7d_1#8 240 sssvlteldk iegvferpsd evirelsral rqalgvslfg idiiinnqtg
TARGET h hhhhhhhhhh hhhh ssss ssss
2q7d_1#8 h hhhhhhhhhh hhhh ssss ssssss
TARGET 267 NVFYVIDINY FPGYGKLPDY EQVFVDFFQN LAQV ----- ----------
2q7d_1#8 290 q-havidina fpgyegvsef ---ftdllnh iatvlqgqst amaatgdval
TARGET sssssss s hhhhhhh hhhh
2q7d_1#8 s ssssssss s hh hhhhhhh hhhhhhhhh
Template's ligands section
Ligands in the template:ANP : 1,MN : 2,SO4 : 7.
Ligands in the template that will be assessed: ANP10, MN1, MN2.
Model's ligands section
ANP10
ANP10 interacts, within a radius of 3 Angstroem, with the following ions: MN1, MN2. They will be considered as a single ligand.
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand z.ANP10 will not be included in the model.
ANP10: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2q7d 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: 2q7d.pdb1.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 0.506 (>0.5 indicates similarity)
Model was succesfully built as MONOMER.
Template Selection
- Start SMR-Pipeline for:99fc7e875c03935922464a9a684307af on BC2-cluster at Tue Feb 19 11:18:16
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:1): model based on new templates
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *************************************************************
- building model based on 2q7dA (83-382) 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:99fc7e875c03935922464a9a684307af on BC2-cluster at Tue Feb 19 11:20:23
2013
Template Search
| Template Description |
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3vot: CRYSTAL STRUCTURE OF L-AMINO ACID LIGASE FROM BACILLUS LIC Solved by: X-RAY, Resolution: 1.80A, 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.