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 P LVLSFHGYTG SGKNYVAEII ANNTFRLGLR
3b85A 116 virpktlgqk hyvdaidtnt ivfgl-gpag sgktylaxak avqalqskqv
TARGET hhhhhhhh hhhhhhh
3b85A hhhh hhhhhhh s sssss s hhhhhhhh hhhhhhh
TARGET 32 STFVQHIVAT NDFPDKNKLE EYQVE----- --------LR NRILTTVQKC
3b85A 165 sri---iltr paveageklg flpgdpylrp lhdalrdxve pevipklxea
TARGET hhhhh
3b85A ss ssss hhhhh hhhhhh hhhhhhhhh
TARGET 69 QR-------- --------SI FIFDEADKLP EQLLGAIKPF LDYY -----
3b85A 218 givevaplay xrgrtlndaf vildeaqntt paqxkxfltr lgfgskxvvt
TARGET hhhhhhhhh
3b85A ssssssshh ss sssss hhhhhhhhh sssss
TARGET ---------- ---------- ---------- ---------- -
3b85A 268 gdglrlvrhi lrgvddvhfs eltssdvvrh qlvghivday e
TARGET
3b85A s hhhhhh sssss ss hhhhhhhhh
Template's ligands section
Ligands in the template:SO4 : 2.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3b85 is annotated as HEXAMER
PISA was used to annotate the quaternary structure, because the author assignment was not complete
A biological unit file could be identified with the same complex description as the PISA annotation and was used to build the assembly: 3b85.pdb1.gz
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 15.200) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode
The target structure was calculated as SINGLE CHAIN
Template Selection
- Start SMR-Pipeline for:139f66dfacc959dbef26c7e9ecd9f690 on BC2-cluster at Wed Feb 20 21:05:41
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 A found
- No template with A found
- No template with B found
- No template with B found
- No template with B found
- 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 3b85A (103-198) 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:139f66dfacc959dbef26c7e9ecd9f690 on BC2-cluster at Wed Feb 20 21:06:40
2013
Template Search
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2rgx: CRYSTAL STRUCTURE OF ADENYLATE KINASE FROM AQUIFEX AEOLICUIN COMPLEX WITH AP5A Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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2rh5: STRUCTURE OF APO ADENYLATE KINASE FROM AQUIFEX AEOLICUS Solved by: X-RAY, Resolution: 2.48A, Identified by HHSEARCH |
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3sr0: CRYSTAL STRUCTURE OF THE PHOSPHORYL TRANSFER TRANSITION STTHE ADENYLATE KINASE: ADP/ALF4/AMP IN THE ACTIVE SITE Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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3b85: CRYSTAL STRUCTURE OF PREDICTED PHOSPHATE STARVATION-INDUCEATPASE PHOH2 FROM CORYNEBACTERIUM GLUTAMICUM Solved by: X-RAY, Resolution: 2.35A, 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.