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
TARGET 1 ESPAFL SAKDEGSFAY LTIKDRTPQI LTKVIDTLHR HKSEFFEKHG
3pt1A 0 hx--tipgrf xtidkgtfge ytastrwpii iqnaiddlsk hqet--eksn
TARGET sss ss hhh hhhhhhhhhh hhhhhhhhhh hh
3pt1A sss ss hhh hhhhhhhhhh hhhhhhhhhh hhh
TARGET 47 EEGIEAEKKA ISLLSKLRNE LQTDKPITPL VDKCV----D THIWNQYLEY
3pt1A 46 gtkfeqgevi kkelkefrqe iidrvplrpf teeeikianv plsfneylkk
TARGET hhhhhhhhh hhhhhhhhhh hhh sss hhhhhh
3pt1A hhhhhhhhh hhhhhhhhhh hhh sss hhhhhhh hhhhhhhh
TARGET 93 QRSLLNEGDG EPRWFFSPWL FVECYMYRRI HEAIMQSPPI HDFDVFKESK
3pt1A 96 h--------p evnwgavewl fsevylyrrv nvlfqrqcew akfdifnrlk
TARGET sss sssh hhhhhhhhhh hhhhh hhhhh
3pt1A sss sssh hhhhhhhhhh hhhhh hhhhh
TARGET 143 EENFFESQGS IDALCSHLLQ LKPVK---GL REEQIQDEFF KLLQISLWGN
3pt1A 138 qstfessfyg vvelalryen llpqlrexkq nddilkvlfk efieislwgn
TARGET hhhh hhh hhhhhhhhhh hh hhhhhhh hhhhhhhh
3pt1A hhhh hhh hhhhhhhhhh hhhhhhhhh hhhhhhhh hhhhhhhh
TARGET 190 KCDLSLSGGE SSSQ--KANI INCLQDLKPF ILINDTESLW ALLSKLKKTV
3pt1A 193 atdlslltna tlediksiqg akaraasesk ivvndtekaw evltkarada
TARGET hhh hh hhhhhhhhh hhhh hhhhhhhh
3pt1A hhh hhhh hh hhhhhhhhh hhhh hhhhhhhh
TARGET 238 ETPVVRVDIV LDNSGFELIT DLVLADFLFS SELATEIHFH GKSIPWFVSD
3pt1A 243 nsreirvdfv ldnsgfelya dlxlaafllq sglatkcifh akdipyxvsd
TARGET ssssss ssss hhhhh hhhhhhhhhh h sssss s ss
3pt1A ssssss ssss hhhhh hhhhhhhhhh h sssss s ss
TARGET 288 VTEHDFNWIV EHMKSSN--- --------LE SMSTCGACWE AYARMGRWAY
3pt1A 293 vxlkdfdilv hdlrdreffp sgepstkesr aldlfagexe kfvssgkief
TARGET s hhhhhhh hhhh hhhhhhhhhh hhhhh ssss
3pt1A s hhhhhhh hhhh hhhh hhhhhhhhhh hhhhh ssss
TARGET 327 HDHAFWTLPH PYCVMPQVA- ----PDLYAE LQKAHLILFK GDLNYRKLMG
3pt1A 343 redsfwttel dywnldanet kyhgsilhkd lqksnlvifk gdlnyrkltg
TARGET s hhh hh hhhh hh sssss shhhhhhhh
3pt1A s hhhhhhh hh sssss shhhhhhhh
TARGET 372 DRKWKFTFPF HQALSG--FH PAPLCSIRTL KCELQVGLQP GQAEQLTASD
3pt1A 393 drkwprttkw etaigplatn gitslslrtc kadvqvalpe gldaklsqew
TARGET sss h hhhh ssssssss hhhhhhhh
3pt1A sss h hhh ssssssss hhhhhhhhh
TARGET 420 --------PH WLTTGRYGIL QFDGPL
3pt1A 443 ekenpgrgsw wccsgkwavi cfcsgi-
TARGET ssss sss
3pt1A hhh ssss sss
Template's ligands section
Ligands in the template:F6P : 1,MG : 1.
Ligands in the template that will be assessed: MG1002.
Model's ligands section
MG1002
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: 0.070
Given the properties calculated previously, the ligand A.MG1002 will be included in the final model.
MG1002: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
3pt1 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: 3pt1.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 0.244 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:c253701c69b75747a8c17a6cd5bebdee on BC2-cluster at Wed May 8 02:49:31
2013
- Found BLAST templates: 1
- 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 modified template library
- Summarize templates:
- Send 1 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ********************************************************************************
- building model based on 3pt1A (3-439) 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:c253701c69b75747a8c17a6cd5bebdee on BC2-cluster at Wed May 8 03:13:10
2013
Template Search
| Template Description |
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3pt1: STRUCTURE OF DUF89 FROM SACCHAROMYCES CEREVISIAE CO-CRYSTAF6P. Solved by: X-RAY, Resolution: 1.77A, Identified by HHSEARCH |
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2ffj: CRYSTAL STRUCTURE OF (2649480) FROM ARCHAEOGLOBUS FULGIDUSAT 2.45 A RESOLUTION Solved by: X-RAY, Resolution: 2.45A, Identified by HHSEARCH |
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2g8l: CRYSTAL STRUCTURE OF A PROTEIN OF UNKNOWN FUNCTION FROM DUF180 FAMILY (3258004) FROM PYROCOCCUS HORIKOSHII AT 2.0A RESOLUTION. Solved by: X-RAY, Resolution: 2.04A, Identified by HHSEARCH |
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1xfi: X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G17340 Solved by: X-RAY, Resolution: 1.70A, Identified by HHSEARCH |
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2q40: ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G17340 Solved by: X-RAY, Resolution: 1.70A, 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.