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 RKAVV NTLERRLFYI PSFKIYSGVA GLFDYGPPGC AIKSNVLSFW
2zt5A 64 ivd--rakme dtlkrrffyd qafaiyggvs glydfgpvgc alknniiqtw
TARGET hhhh hhhhhh sss ss ssssshhhh hhhhhhhhhh
2zt5A hhhhh hhhhh sss ssshhhh hhhhhhhhhh
TARGET 46 RQHFILEENM LEVDCPCVTP EVVLKASGHV DKFTDLMVKD EKTGTCYRAD
2zt5A 112 rqhfiqeeqi leidctmltp epvlktsghv dkfadfmvkd vkngecfrad
TARGET hhhhhhhh sss ssss shhhhhh ssssssss s sssh
2zt5A hhhhhhhh sss ssss shhhhh ssssssss s sssh
TARGET 96 HLLKDYCTEK LEKDLTISAE KAAELKDVLA VMEDFSPEQL GAKIREYGIT
2zt5A 162 hllkah-lqk lmsdkkcsve kksemesvla qldnygqqel adlfvnynvk
TARGET hhhh hh hh hhhhhhhhh hhhh hhhhhhh
2zt5A hhhhhh hhh hh hh hhhhhhhhh hhhh hhhhhh
TARGET 146 APDTKNPLSD PYPFNLMFQT SIGPSGLIPG YMRPETAQGI FVNFKDLYYY
2zt5A 211 spitgndlsp pvsfnlmfkt figpggnmpg ylrpetaqgi flnfkrllef
TARGET sss sssss sss ss sss sss hhh h hhhhh
2zt5A sss sssss s ss sss sss hhhh hhhhhh
TARGET 196 NGKKLPFAAA QIGQAFRNEI SPRQGLLRVR EFTLAEIEHF VDPENKSHPK
2zt5A 261 nqgklpfaaa qignsfrnei sprsglirvr eftmaeiehf vdpsekdhpk
TARGET ssss sssssss s ssssssssss s h
2zt5A ssss sssssss s ssssssssss s h
TARGET 246 FSDVAKLEFL MFPREEQMSG QSAKKLCLGE AVAKGTVNNE TLGYFIGRVY
2zt5A 311 fqnvadlhly lysakaqvsg qsarkmrlgd aveqgvinnt vlgyfigriy
TARGET hh ssss ss hhhhh ssssshh hhhh hhhhhhhhhh
2zt5A hh ssss ss hhhhh ssssshh hhh hhhhhhhhhh
TARGET 296 LFLTRLGIDK ERLRFRQHLA NEMAHYAADC WDAEIESSYG WIECVGIADR
2zt5A 361 lyltkvgisp dklrfrqhme nemahyacdc wdaesktsyg wieivgcadr
TARGET hhhhhh sssssss ss sssssss s ssssssssss
2zt5A hhhhhh sssssss ss sssssss s sssssssss
TARGET 346 SAYDLRAHSD KSGTPLVAEE KFAEPKEVEK LVITP ---- ----------
2zt5A 411 scydlschar atkvplvaek pyve--evvp nviepsfglg rimytvfeht
TARGET hhhhhhh hh sssss
2zt5A hhhhhhh hh sss s ss sssssssssh hhhhhhhhhs
TARGET ---------- ---------- ---------- ---------- ----------
2zt5A 539 fhvregdeqr tffsfpavva pfkcsvlpls qnqefmpfvk elsealtrhg
TARGET
2zt5A ssssss sss ssss sssssss hhhhhhh hhhhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
2zt5A 589 vshkvddssg sigrryartd eigvafgvti dfdtvnktph tatlrdrdsm
TARGET
2zt5A sssss hhhhhhhhh h ssssss hhh s sssssss
TARGET ---------- ---------- ---------- -----
2zt5A 639 rqiraeisel psivqdlang nitwadvear yplfe
TARGET
2zt5A ssssssshhh hhhhhhhhh hhhhhhh
Template's ligands section
Ligands in the template:B4P : 1.
Ligands in the template that will be assessed: B4P1101.
Model's ligands section
B4P1101
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 A.B4P1101 will not be included in the model.
B4P1101: conservation:False, RMSD:False, included: False
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2zt5 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: 2zt5.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 0.246 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:92f28cbb80740ff5a6bd1e4195128884 on BC2-cluster at Tue Feb 19 14:21:55
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 C found
- No template with D found
- No template with C found
- No template with D found
- No template with C found
- No template with D found
- Proof template(s) selection compared to previous Repository update
- Different number of templates selected (old0 vs new:4): model based on new templates
- Send 4 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ******************************************
- building model based on 2zt5A (117-496) was successful
- ****************
- building model based on 2pmfA (571-720) was successful
- *****************************************************************
- building model based on 4hvcB (118-708) was not successful go to next best template
- *****************************************************************
- building model based on 4hvcA (117-708) was not successful go to next best template
- ********************************************************
- building model based on 3qo5A (120-627) was not successful go to next best template
- ********************************************************
- building model based on 3qo8A (121-626) was not successful go to next best template
- ****************************************************************
- building model based on 3qneA (45-626) was not successful go to next best template
- ****************************************************************
- building model based on 3qo7A (45-626) was not successful go to next best template
- 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:92f28cbb80740ff5a6bd1e4195128884 on BC2-cluster at Tue Feb 19 14:41:55
2013
Template Search
| Template Description |
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4ex5: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE LYSRS FROM BURKTHAILANDENSIS BOUND TO LYSINE Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH |
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4hvc: CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE IN COMPLHALOFUGINONE AND ATP ANALOGUE Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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3qo7: CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM CANDID Solved by: X-RAY, Resolution: 2.55A, Identified by HHSEARCH |
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3qne: CANDIDA ALBICANS SERYL-TRNA SYNTHETASE Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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3qo5: CRYSTAL STRUCTURE OF THE SERYL-TRNA SYNTHETASE FROM CANDID Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH |
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3qo8: CRYSTAL STRUCTURE OF SERYL-TRNA SYNTHETASE FROM CANDIDA AL Solved by: X-RAY, Resolution: 2.00A, 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.