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 LLRF LRLVGQLKRV PRTGWVYRNV EKPESVSDHM YRMAVMAMVT
4dmbA 13 gars--llqf lrlvgqlkrv prtgwvyrnv qrpesvsdhx yrxavxaxvi
TARGET hhh hhhhhhh s ss hhhh ssshhhh hhhhhhhh
4dmbA hhh hhhh hhhhhhh s ss hhhh ssshhhh hhhhhhhh
TARGET 45 RDDRLNKDRC IRLALVHDMA ECIVGDIAPA DNIPKEEKHR REEEAMKQIT
4dmbA 61 kddrlnkdrc vrlalvhdxa ecivgdiapa dnipkeekhr reeeaxkqit
TARGET hhhh hhhhh h h hhhhhh hhhhhhhhhh
4dmbA hhhh hhhhhh h h hhhhhh hhhhhhhhhh
TARGET 95 QLLPEDLRKE LYELWEEYET QSSEEAKFVK QLDQCEMILQ ASEYEDLENK
4dmbA 111 qllpedlrke lyelweeyet qssaeakfvk qldqcexilq aseyedlehk
TARGET h hhhhhh hhhhhhhhhh hhhhhhh hhhhhhhhhh hhhhhhhh
4dmbA h hhhhhh hhhhhhhhhh hhhhhhh hhhhhhhhhh hhhhhhhh
TARGET 145 PGRLQDFYDS TAGKFSHPEI VQLVSELETE RNASMATASA
4dmbA 161 pgrlqdfyds tagkfnhpei vqlvseleae rstniaaaas -
TARGET hhhhh hhh hhhhhhhhhh hhhhhhhhh
4dmbA hhhhh hhh hhhhhhhhhh hhhhhhhhh
Template's ligands section
Ligands in the template:GOL : 1,MG : 2,NO3 : 1,PEG : 1,PO4 : 1.
Ligands in the template that will be assessed: MG306, MG307.
Model's ligands section
MG306
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: 0.060
Given the properties calculated previously, the ligand A.MG306 will be included in the final model.
MG306: conservation:True, RMSD:True, included: True
MG307
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand A.MG307 will not be included in the final model.
MG307: conservation:False, RMSD:False, included: False
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
4dmb 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: 4dmb.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 (=DIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.364 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 4dmbB
Template Selection
- Start SMR-Pipeline for:521e6148e505b9b4c4cbc252b4f8b266 on BC2-cluster at Sat Feb 23 02:14:24
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 1 go for
modeling ...
- 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 4dmbA (12-195) 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:521e6148e505b9b4c4cbc252b4f8b266 on BC2-cluster at Sat Feb 23 02:15:26
2013
Template Search
| Template Description |
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4dmb: X-RAY STRUCTURE OF HUMAN HEPATITUS C VIRUS NS5A-TRANSACTIV2 AT THE RESOLUTION 1.9A, NORTHEAST STRUCTURAL GENOMICS C(NESG) TARGET HR6723 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.