SWISS-MODEL Repository
Uniprot features:
SWISS-MODEL Repository - Model Details
Model Overview
Sequence
| UniProt | Q9M041 |
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 PERH ENVVLEYLDN IVVINDQYPK ARKHVLVLAR
3sp4B 29 gshmsfrdnl kvyiespesy knviy-yddd vvlvrdmfpk skmhlllmtr
TARGET sss s ssssss ssssssss
3sp4B hhhhh ssss ss s ssssss ssssssss
TARGET 35 QESLDGLEDV RKENLQLLQE MHNVGLKWVD RFQNEDASLI ----------
3sp4B 78 dphlthvhp- ----leimmk hrslveklvs yvqgdlsgli fdearnclsq
TARGET hhh hhh hhhhhhhhh hhh
3sp4B h hhhh hhhhhhhhh hhhh hhh hhhhhhh
TARGET 75 ---------- FRLGYHSVPS MRQLHLHVIS QDFNSDSLKN KKHWNSFTTS
3sp4B 123 qltnealcny ikvgfhagps mnnlhlhimt ldhvspslkn sahyisftsp
TARGET ssssss sssss hhhhh
3sp4B hhhhh s sssssss sssss s hhhhhh
TARGET 115 FFRDSVDVLE EVNSQGKANV ASEDLLKGEL RCNRC-RSAH PNIPKLKSHV
3sp4B 173 ffvkidtpts nlptrgtlt- ---slfqedl kcwrcgetfg rhftklkahl
TARGET sssss hh s ss sss hhhhhhhh
3sp4B sssss hhhhh hhh s ss sss hhhhhhhh
TARGET 164 RSCHSQFPD ----
3sp4B 219 qeeyddwldk svsm
TARGET hhhhhhhhh
3sp4B hhhhhhhhhh
Template's ligands section
Ligands in the template:SO4 : 1,ZN : 1.
Ligands in the template that will be assessed: ZN601.
Model's ligands section
ZN601
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 B.ZN601 will not be included in the final model.
ZN601: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3sp4 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: 3sp4.pdb2.gz
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 27.461) 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:99c092d8c0263ef729efe4154218306a on BC2-cluster at Tue Feb 19 20:14:16
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:
- Warning: Oligomer Prediction was not successfull!
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:5): model based on new templates
- Send 5 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ***************
- building model based on 3sp4A (727-898) was not successful go to next best template
- ***************
- building model based on 3sp4B (727-898) was successful
- *********
- building model based on 4ablA (516-615) was successful
- **************
- building model based on 4gp7B (223-381) was successful
- ***********
- building model based on 4abkA (518-644) was successful
- ****
- building model based on 4ablA (453-498) 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:99c092d8c0263ef729efe4154218306a on BC2-cluster at Tue Feb 19 20:16:50
2013
Template Search
| Template Description |
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4gp6: POLYNUCLEOTIDE KINASE Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH |
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4gp7: POLYNUCLEOTIDE KINASE Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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4abl: HUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3 Solved by: X-RAY, Resolution: 1.15A, Identified by HHSEARCH |
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4abk: HUMAN PARP14 (ARTD8, BAL2) - MACRO DOMAIN 3 IN COMPLEX WITADENOSINE-5-DIPHOSPHORIBOSE Solved by: X-RAY, Resolution: 1.60A, 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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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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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.