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 VNPDLQKE RSTATFNPRE FSVLWAGGEE RFKEKKALEK LFLEDPALQD
1is2A 1 mnpdlrke rasatfnpel ithildgspe ntrrrreien lilndpdfqh
TARGET hhhhhh hh hh hhhhh hh hhhhhhhhhh hhh
1is2A hhhhhh hh hh hhhhh hh hhhhhhhhhh hhh
TARGET 49 DLPISYLSHK ELYEHSLRKA CIIGEKIRK- LRADGEDGVD TYNALLGGSL
1is2A 49 e-dynfltrs qryevavkks atmvkkmrey gisdpeeimw fknsvhrg--
TARGET hh hhhhhhhhhh hhhhhhh hhhhhh hhhhhh
1is2A hh hhhhhhhhhh hhhhhhhhhh hhhhhh hhhhhh
TARGET 98 GSAILKEGNP LALHYVMFVP TIMGQGTMDQ QVEWLSKAWD CEIIGTYAQT
1is2A 96 ------hpep ldlhlgmflp tllhqataeq qerffmpawn leitgtyaqt
TARGET hhhh hh hhhh hhh hhhhhhhh sssss s
1is2A hhhh hh hhhh hhh hhhhhhhh sssss s
TARGET 148 ELGHGTFLRG LETRADYDAS TQEFVINTPS LSAYKWWPGG LGHTANHAVV
1is2A 140 emghgthlrg lettatydpk tqefilnspt vtsikwwpgg lgktsnhaiv
TARGET ss ssssss sssssss sssssss sssss
1is2A ss ssssss sssssss sssssss sssss
TARGET 198 VAQLYTKGEF RGLAPFIVQL RDSDTHRPMP GIDIGDIGTK LGMKGVNNGY
1is2A 190 laqlitqgec yglhafvvpi reigthkplp gitvgdigpk fgyeemdngy
TARGET ssssss ss ssssssssss ss sss sssssss ssss
1is2A ssssss ss ssssssssss ss sss sssssss ssss
TARGET 248 LGLKNVRVPL NNMLMKNQQV LPDGTYVAPK NSVLTYGTMM FVRCALIRDT
1is2A 240 lkmdnyripr enmlmkyaqv kpdgtyvkk- ---ltygtmv fvrsflvgna
TARGET ssssssssss sss ss s sss hhhhh hh hhhhh
1is2A ssssssssss sss ss s sss hhhhh hh hhhhh
TARGET 298 AQSLAKASTI ATRYSAVRRQ SPIDPNQPEP QIMDHTTQQL KLFPQIAKAI
1is2A 290 aqslskacti airysavrrq seikqsepep qildfqtqqy klfpllatay
TARGET hhhhhhhhhh hhhhhhhsss s ss hhhhh hhhhhhhhhh
1is2A hhhhhhhhhh hhhhhhhsss s ss hhhhh hhhhhhhhhh
TARGET 348 VFKTTGDGIW NMYNVISGEI EQGNLDRLPE MHALSCCLKA ICSADAAAGV
1is2A 340 afhfvgrymk etylrinesi gqgdlselpe lhaltaglka fttwtanagi
TARGET hhhhhhhhhh hhhhhhhhhh hh hhhh hhhhhhhhhh hhhhhhhhhh
1is2A hhhhhhhhhh hhhhhhhhhh hh hhhh hhhhhhhhhh hhhhhhhhhh
TARGET 398 ETCRLSCGGH GYMDCSNFPT IYGMTTAVCT YEGENTVMLL QTARYLVKVY
1is2A 390 eecrmacggh gyshssgipn iyvtftpact fegentvmml qtarflmkiy
TARGET hhhhhh h h hh hhhhhhhh hhhhhh hhhhhhhhhh
1is2A hhhhhh h h hh hhhhh hhhhhh hhhhhhhhhh
TARGET 448 GQALNGEKLV PTVSYISDAI NQTKFVNFDG SLRSIVKAFQ FVAANKTRIA
1is2A 440 dqvrsgklvg gmvsylndlp s----vdin- sleglteayk lraarlveia
TARGET hhhhh hhh hhhhhhhh hhhhhhhhhh
1is2A hhhh hhh hhhhhhhhh hhhhhhhhhh
TARGET 498 YEQIELRRKQ GYGTEVAANL CGTFLTAAAD LHGRAFLAQT AYTELLALSR
1is2A 499 aknlqthvsh rkskevawnl tsvdlvrase ahchyvvvkv fsdklpkiqd
TARGET hhhhhhhh hhhhh hhhhhhhhh hhhhhhhhhh hhhhhh
1is2A hhhhhhhh hhhhh hhhhhhhhh hhhhhhhhhh hhhhhh
TARGET 548 EVSPELAEVL KVVLELYLVD ACLNRIGDFL RFIDLTDQDV TKLEVRLENC
1is2A 549 ka---vqavl rnlcllysly gisqkggdfl egsiitgaql sqvnarilel
TARGET hhhh hhhhhhhhhh hhh hhhh hh hhhh hhhhhhhhhh
1is2A hh hhhhh hhhhhhhhhh hhh hhhh h hhhh hhhhhhhhhh
TARGET 598 LKRFRPNAVS LVDSFDLHDR VLDSALGAYD GNVYEHIFES TKKNPLNKEP
1is2A 596 ltlirpnava lvdafdfkdm tlgsvlgryd gnvyenlfew akksplnkte
TARGET hhhhh hh hhhh hh hh hhhhhhh hhh
1is2A hhhh hhh hhhh hh hh hhhhhhh hhh
TARGET 648 VNGAFHKYLK
1is2A 646 vhesyhkhlk -
TARGET hhhh
1is2A hhhh
Template's ligands section
Ligands in the template:FAD : 2.
Ligands in the template that will be assessed: FAD1699, FAD699.
Model's ligands section
FAD699
The ligand binds less than 3 template residues.
Given the properties calculated previously, the ligand FAD699 will not be included in the model.
FAD699: conservation:False, RMSD:False, included: False
FAD1699
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: 0.030
Given the properties calculated previously, the ligand FAD1699 will be included in the model.
FAD1699: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
1is2 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: 1is2.pdb1.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template can be assumed to be similar (=DIMER)
The corresponding reliability score is 0.83 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1is2B
Unfortunately, we were not able to built the model as DIMER.
Thus, the model was built as single chain.
Template Selection
- Start SMR-Pipeline for:107459c646f962806d65d6ee448fd62a on BC2-cluster at Fri Feb 22 09:30:03
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
FATAL - No A3m found
- 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:1): model based on new templates
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- *******************************************************************************
- Oligomeric modeling of 1is2A was not successful, fall back to monomeric modeling
- building model based on 1is2A (6-662) 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:107459c646f962806d65d6ee448fd62a on BC2-cluster at Fri Feb 22 09:43:20
2013
Template Search
| Template Description |
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3pfd: CRYSTAL STRUCTURE OF AN ACYL-COA DEHYDROGENASE FROM MYCOBATHERMORESISTIBILE BOUND TO REDUCED FLAVIN ADENINE DINUCLEBY COMBINED IODIDE ION SAD MR Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH |
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4hr3: STRUCTURE OF A PUTATIVE ACYL-COA DEHYDROGENASE FROM MYCOBAABSCESSUS Solved by: X-RAY, Resolution: 1.80A, 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.