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 IVDLQ GGYADKASGR
1yqsA 3 lpapddtglq avlhtalsqg apgamvrvdd ngt--ihqls egvadratgr
TARGET ssss ss
1yqsA hhhhh hhhhhhhhh sssssssss s s sssss sssss ss
TARGET 16 KWTPDTRTVV FSTTKAVGAV CVAMLVDRGH ISYDDKMSKI WPEFAQNGKE
1yqsA 51 aitttdrfrv gsvtksfsav vllqlvdegk ldldasvnty lpgllpd--d
TARGET ss hhhhhhhh hhhhhhhh hhh
1yqsA ss sss hhhhhhhh hhhhhhhh hhh
TARGET 66 NITIDWLMSH RAGL ----- ---------- ---------- ----------
1yqsA 99 ritvrqvmsh rsglydytnd mfaqtvpgfe svrnkvfsyq dlitlslkhg
TARGET hhhhh
1yqsA hhhhhh hhh h hhhhhh hh h hhhhhhh
TARGET ---------- ---------- ---------- ---------- ----------
1yqsA 149 vtnapgaays ysntnfvvag mliekltghs vateyqnrif tplnltdtfy
TARGET
1yqsA h hhh hhhhhhh hhhhhhh hhh
TARGET ---------- ---------- ---------- ---------- ----------
1yqsA 199 vhpdtvipgt hangyltpde aggalvdste qtvswaqsag avisstqdld
TARGET
1yqsA ssss sss sss hhhhh
TARGET ---------- ---------- ---------- ---------- ----------
1yqsA 249 tffsalmsgq lmsaaqlaqm qqwttvnstq gyglglrrrd lscgisvygh
TARGET
1yqsA hhhhhhhh hhhhhhh sss ss sss sssss s ssssss
TARGET ---------- ---------- ---------- ---------- ---------
1yqsA 299 tgtvqgyyty afaskdgkrs vtalantsnn vnvlntmart lesafcgkp
TARGET
1yqsA ssss sssss ssss sss ssssssss hhhhhhhhhh hhhhh
Template's ligands section
Ligands in the template:BSA : 2,GOL : 2.
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
1yqs 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: 1yqs.pdb1.gz
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 37.975) 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
Template Selection
- Start SMR-Pipeline for:fca9b26a69ff266221fd98030a31dfaf on BC2-cluster at Thu Feb 21 08:15:42
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 A found
- No template with A found
- No template with B found
- No template with B 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 1yqsA (103-181) was successful
- ******************
- building model based on 1o07B (109-215) was successful
- ***************************
- building model based on 1i5qB (109-266) was successful
- **************************************************************
- building model based on 3zytA (68-434) 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:fca9b26a69ff266221fd98030a31dfaf on BC2-cluster at Thu Feb 21 08:19:17
2013
Template Search
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3tsg: CRYSTAL STRUCTURE OF GES-14 Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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3v3r: CRYSTAL STRUCTURE OF GES-11 Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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3ni9: GES-2 CARBAPENEMASE APO FORM Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH |
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3nia: GES-2 CARBAPENEMASE TAZOBACTAM COMPLEX Solved by: X-RAY, Resolution: 1.65A, Identified by HHSEARCH |
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3v3s: CRYSTAL STRUCTURE OF GES-18 Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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4hes: STRUCTURE OF A BETA-LACTAMASE CLASS A-LIKE PROTEIN FROM VEPARVULA. Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH |
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2qpn: GES-1 BETA-LACTAMASE Solved by: X-RAY, Resolution: 1.10A, Identified by HHSEARCH |
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3p09: CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM FRANCISELLA TULAR Solved by: X-RAY, Resolution: 1.90A, 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.