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 I
2eefA 1 gssgssgaes esfvldfsqp sadyldfrnr lqadhvclen cvlkdka--i
TARGET s
2eefA sssss hhhhhhh hhh ssss ssss ss s
TARGET 2 TGLVYVKNLS FEKYLEIKFT FNSWRDIHYV TANFNRTINS NVDEFKFTID
2eefA 49 agtvkvqnla fektvkirmt fdtwksytdf pcqyvkdtya gsdrdtfsfd
TARGET ssss sssssss s sssss sssss
2eefA sssss sssssss sss sssss sssss
TARGET 52 LNSLKYILLI KRIITMEKNT SSCPLNIELC CRYDVNNETY YDNNNGKNYH
2eefA 99 is------lp ekiqsyer-- ------mefa vyyecngqty wdsnrgknyr
TARGET s sss sssss sss ss
2eefA ss s sss sssss sss ss s
TARGET 102 LFMTTFK -- ---------- --
2eefA 135 iiraelkstq gmtkphsgpd lg
TARGET
2eefA ssss
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
2eef is annotated as MONOMER
The template structure (2eef) was solved by NMR and does not contain any quaternary structure annotation
The template is annotated by the number of chains found in the PDB file
Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 28.704) 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:7906c764139cbccf6ce14d9d9fa4fb42 on BC2-cluster at Mon Feb 18 20:47:17
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:
- Warning: Oligomer Prediction was not successfull!
- 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
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- ***********
- building model based on 2eefA (258-365) 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:7906c764139cbccf6ce14d9d9fa4fb42 on BC2-cluster at Mon Feb 18 20:48:36
2013
Template Search
| Template Description |
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4eib: CRYSTAL STRUCTURE OF CIRCULAR PERMUTED CBM21 (CP90) GIVES THE ALTERED SELECTIVITY ON CARBOHYDRATE BINDING. Solved by: X-RAY, Resolution: 1.86A, Identified by HHSEARCH |
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2v8m: CARBOHYDRATE-BINDING OF THE STARCH BINDING DOMAIN OF RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH BETA- CYCLODEXTRIN AND MALTOHEPTAOSE Solved by: X-RAY, Resolution: 99.9A, Identified by HHSEARCH |
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2vq4: CARBOHYDRATE-BINDING OF THE STARCH BINDING DOMAIN OF RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH BETA- CYCLODEXTRIN AND MALTOHEPTAOSE Solved by: X-RAY, Resolution: 99.9A, Identified by HHSEARCH |
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2v8l: CARBOHYDRATE-BINDING OF THE STARCH BINDING DOMAIN OF RHIZOPUS ORYZAE GLUCOAMYLASE IN COMPLEX WITH BETA- CYCLODEXTRIN AND MALTOHEPTAOSE Solved by: X-RAY, Resolution: 99.9A, Identified by HHSEARCH |
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2djm: SOLUTION STRUCTURE OF N-TERMINAL STARCH-BINDING DOMAIN OF GLUCOAMYLASE FROM RHIZOPUS ORYZAE Solved by: NMR, 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.