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 ] |
Alignment
3vstC 1 meyhvaktgs degkgtlkdp fltinkaasv amagdtiivh egvyrewvkp
3vstC sssss hhhh ssssss sssss
3vstC 51 kykglsdkrr itykaaegek vvikgseriq swqrvegnvw rcqlpnsffg
3vstC ssssss s sssssssss sss sss sssssshh
3vstC 101 efnpykeevf gdwlltvnek khlgdvylng msfyevtnye dlfnpqlrte
3vstC sss sss sss sssss ssssss h hh ss
3vstC 151 vldhwtqkiv piknaeqtky vwyaevdrek ttiyanfqga dpneefvein
3vstC sss sss ss hhh s sssssss ss sssssss sssss
3vstC 201 vrrscfypve tgidyitvkg femahaatpw apptadqpgl igpnwskgwi
3vstC s ssssss sssss ss
3vstC 251 iedniihdak csaisigkea ttgnnyrsir kdkpgyqyql eavfnakrng
3vstC sssssss ss s sssss hhhhh hhhhhh hhhhhhhh
TARGET 1 QLLNVEIQN FGSPLYSSVE FSNVSAGSWI ISSTLHQSC-
3vstC 301 wskekigsh- -iirnntiyd cgqnaivg-- -hlggvfsei ynnhiynial
TARGET ssssss sss sss s ssss
3vstC s ssssssss sssssss ss sss ssssss
TARGET 39 --------GG GIHAAASHGV LLNDNIVFGT AGHGIDLEGQ A--YTVTNNL
3vstC 346 krefygheia giklhaaidv qihhnrihdc s-lglwldwe aqgtrvsknl
TARGET ssss s ssssssss sssss sss s
3vstC sss sssss s ssssssss ssssss sssssss
TARGET 79 VV ------- ---------- ---------- ---------- ----------
3vstC 395 fynnnrdvfv evshgpylvd hnilsseyai dnmsqggayi nnliagkmnq
TARGET ss
3vstC ss ssss ss ssss sssss ss sss sssss sssss ssss
TARGET ---------- ---------- ---------- ---------- ----------
3vstC 445 rkvlnrstqy hlphstevag fafvyggddr fynnifigke glenvgtshy
TARGET
3vstC s sss ss ssss ss ss ss sssss
TARGET ---------- ---------- ---------- ---------- ----------
3vstC 495 nncttsleey iekvnevpgd lgeferveqp vyinknayfn gaepfekekd
TARGET
3vstC hhhh hhhh hhhhh sss ssss
TARGET ---------- ---------- ---------- ---------- ----------
3vstC 545 nlvkkdfdpk laiidegdev ylslqlpdef enivgdihst ktlervrivd
TARGET
3vstC sss sssss ss ssssss hh h sss
TARGET ---------- ---------- ---------- ---------- ----
3vstC 595 aeyespdgke lvldtdylda kkpenssigp iallkkgnny ikvw
TARGET
3vstC ssssss s ss ssss sss
Template's ligands section
Ligands in the template:BXP : 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
3vst is annotated as TETRAMER
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: 3vst.pdb1.gz
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 17.582) 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
To build the complex the following chains of the complex has been additionally identified: 3vstB 3vstA 3vstD
Template Selection
- Start SMR-Pipeline for:5184e3c25d6453985fe161a12d4fc113 on BC2-cluster at Mon Apr 22 21:34:31
2013
- Analyze BLAST summary ...
- No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH
- No A3m found
- 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:2): model based on new templates
- Send 2 Templates for modeling
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- **
- building model based on 3vstC (2987-3066) was successful
- **
- building model based on 4gq7A (368-476) 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:5184e3c25d6453985fe161a12d4fc113 on BC2-cluster at Mon Apr 22 21:39:01
2013
Template Search
| Template Description |
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3vsu: THE COMPLEX STRUCTURE OF XYLC WITH XYLOBIOSE Solved by: X-RAY, Resolution: 2.05A, Identified by HHSEARCH |
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3vsv: THE COMPLEX STRUCTURE OF XYLC WITH XYLOSE Solved by: X-RAY, Resolution: 2.05A, Identified by HHSEARCH |
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3vst: THE COMPLEX STRUCTURE OF XYLC WITH TRIS Solved by: X-RAY, Resolution: 2.05A, Identified by HHSEARCH |
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4gq7: CRYSTAL STRUCTURE OF LG-FLO1P Solved by: X-RAY, Resolution: 2.53A, 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.