SWISS-MODEL Repository 
Uniprot features:
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 ] |
Alignment
1f7uA 2 astanmisql kklsiaepav akdshpdvni vdlmrnyisq elskisgvds
1f7uA hhhhhhhhh hh hhh hh h hhhhhhhhhh hhhhhh h
TARGET 1 DTQDQARR LAEKLKCDTV
1f7uA 52 slifpalewt ntmergdlli piprlrikga --npkdlavq waekfpcgdf
TARGET hhhhhhh hhhh s
1f7uA hhhhhh sss sshh hhhhhhh hhhh s
TARGET 19 VTAISAGPRT LNFKINRELL TKAVLQQVTE DGCKYGLKSE LFSDLPKKRI
1f7uA 100 lekveangpf iqfffnpqfl aklvipdilt rkedyg-sck lven---kkv
TARGET sssssss s sssssshhhh hhhhhhhhhh h sss
1f7uA sssssss ss sssssshhhh hhhhhhhhhh h sss
TARGET 69 VVEFSSPNIA KKFHVGHLRS TIIGNFIANL KEALGHQVTR INYIGDWGMQ
1f7uA 146 iiefsspnia kpfhaghlrs tiiggflanl yeklgwevir mnylgdwgkq
TARGET ssss hhhhh hhhhhhhhhh hhh ssss ss hh
1f7uA ssss hhhhh hhhhhhhhhh hhh ssss ssss hh
TARGET 119 FGLLGTGFQL FGYEEKLQTN PLQHLFDVYV QVNKEATDDK NVTKL-----
1f7uA 196 fgllavgfer ygneealvkd pihhlfdvyv rinkdieeeg dsipleqstn
TARGET hhhhhhhhh hhhhhh hhhhhhhhh hhhh h
1f7uA hhhhhhhhh hhhhhh hhhhhhhhh hhhh h
TARGET 164 --AHEFFHRL EMGDTQALSL WQRFRDLSIE EYTQIYKRLG IYFDEYSG-E
1f7uA 246 gkareyfkrm edgdeealki wkrfrefsie kyidtyarln ikydvysges
TARGET hhhhhh h hhhhhh hhhhhhhhhh hhhhhhh sss
1f7uA hhhhhh h hhhhhh hhhhhhhhhh hhhhhhh sssss
TARGET 211 SFYREKSQDV LKLLDSKGLL QKTAEGNVVV DLSGTGDLSS VCTVMRSDGT
1f7uA 296 qvskesmlka idlfkekglt hed-kgavli dltkfnkklg kaivqksdgt
TARGET hhhhhhh hhhhhhh sss ssss sshhh s ssss
1f7uA hhhhhhh hhhhhhh sss ssss sshhh s ssss
TARGET 261 SLYATRDLAA AIHRMDKYNF DTMIYVADKG QRRHFQQVFQ MLKIMGYDWA
1f7uA 345 tlyltrdvga amdryekyhf dkmiyviasq qdlhaaqffe ilkqmgfewa
TARGET hhhhhhhh hhhhhhh ssssssss hhhhhhhhh hhhh hh
1f7uA hhhhhhhh hhhhhhh ssssssss hhhhhhhhh hhhh hh
TARGET 311 ERCQHVPFGI VKGMKTRRGG VTFLEDVLNE VQSRMLQNMA SIKTTK-QLE
1f7uA 395 kdlqhvnfgm vqgmstrkgt vvfldnilee tkekmhevmk knenkyaqie
TARGET h sssss s ss hhhhhhh hhhhhhhhhh hh
1f7uA h sssss s ss hhhhhhh hhhhhhhhhh hhhh
TARGET 360 NPQETAERVG LAAVIIQDFR GTLLSDYQFS WDRVFQSRGD TGVFLQYTHA
1f7uA 445 hpeevadlvg isavmiqdmq gkrinnyefk wermlsfegd tgpylqyahs
TARGET hhhhhhhhh hhhhhhhhh sss hhhh hhhhhhhh
1f7uA hhhhhhhhh hhhhhhhhh sss hhhh hhhhhhhh
TARGET 410 RLCSLEETFG CGYLN----D SNVACLQEPQ SVSILQHLLR FDEVLYLSSQ
1f7uA 495 rlrsvern-a sgitqekwin adfsllkepa akllirllgq ypdvlrnaik
TARGET hhhhhhh hh hhhhhhhhhh hhhhhhhhhh
1f7uA hhhhhhh hhh hh hhhhhhh hhhhhhhhhh
TARGET 456 DLQPKHIVSY LLTLSHLAAV AHKTLQVKDS PPDVAGARLH LFKAVRSVLA
1f7uA 544 thepttvvty lfklthqvss cydvlwvagq teelatarla lygaarqvly
TARGET h hhhhhh hhhhhhhhhh hh hhhhhhhhh hhhhhhhhhh
1f7uA h hhhhhh hhhhhhhhhh hh hhhhhhhhh hhhhhhhhhh
TARGET 506 NGMKLLGITP VCRM
1f7uA 594 ngmrllgltp verm-
TARGET hhhhhh
1f7uA hhhhhh
Template's ligands section
Ligands in the template:ALA : 1,H2U : 1.
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
1f7u 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: 1f7u.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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.35 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:95b22e4c6fed92e5b8a0099763d426d1 on BC2-cluster at Wed Apr 24 09:55:51
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:2): model based on new templates
- Send 2 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ************************************************************************
- building model based on 1f7uA (60-578) was successful
- ***************************************************************************
- building model based on 1iq0A (31-572) 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:95b22e4c6fed92e5b8a0099763d426d1 on BC2-cluster at Wed Apr 24 10:00:43
2013
Template Search
| Template Description |
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4aq7: TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEAND LEUCYL-ADENYLATE ANALOGUE IN THE AMINOACYLATION CONFO Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH |
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4as1: TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEAND THE BENZOXABOROLE AN2679 IN THE EDITING CONFORMATION Solved by: X-RAY, Resolution: 2.02A, Identified by HHSEARCH |
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4ari: TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEBENZOXABOROLE AN2679 IN THE EDITING CONFORMATION Solved by: X-RAY, Resolution: 2.08A, Identified by HHSEARCH |
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4arc: TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEAND LEUCINE IN THE EDITING CONFORMATION Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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3ziu: CRYSTAL STRUCTURE OF MYCOPLASMA MOBILE LEUCYL-TRNA SYNTHETASE WITH LEU-AMS IN THE ACTIVE SITE Solved by: X-RAY, Resolution: 2.07A, Identified by HHSEARCH |
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3zgz: TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEAND TOXIC MOIETY FROM AGROCIN 84 (TM84) IN AMINOACYLATIONLIKE CONFORMATION Solved by: X-RAY, Resolution: 2.40A, 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.