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 LRYDGRVA VVTGAGAGLG REYALLFAER GAKVVVNDLG GTHSGDGASQ
3omlA 8 lrydgrva vvtgagaglg reyallfaer gakvvvn--- ----------
TARGET sss sss hh hhhhhhhhh ssssssss sss ssss
3omlA sss sss hh hhhhhhhhh sssss
TARGET 49 RAADIVVDEI RKAGGEAVAD YNSVIDGAKV IETAIKAFGR VDILVNNAGI
3omlA 57 -aadivvdei rkaggeavad ynsvidgakv ie-------- --ilvnnagi
TARGET s hhhhhhh hhh sssss hhh h ssss
3omlA hhhhhhh hh sssss hhh h ssss
TARGET 99 LRDRSLVKTS EQDWNLVNDV HLKGSFKCTQ AAFPYMKKQN YGRIIMTSSN
3omlA 106 lrdrslvkts eqdwnlvndv hlkgsfkctq aafpymkkqn ygriimtssn
TARGET hhhhhhhhhh hhhhhhhhhh hhhhhhhhh sssssss h
3omlA hhhhhhhhhh hhhhhhhhhh hhhhhhhhh sssssss h
TARGET 149 SGIYGNFGQV NYTAAKMGLI GLANTVAIEG ARNNVLCNVI VPTAASRMTE
3omlA 156 sgiygnfgqv nytaakmgli glantvaieg arnnvlcnvi vpt------e
TARGET hhh h hhhhhhhhhh hhhhhhhhh sssssss s hhhhhhh
3omlA hhhh h hhhhhhhhhh hhhhhhhhhh h sssssss sss
TARGET 199 GILPDILFNE LKPKLIAPVV AYLCHESCED NGSYIESAAG WATKLHMVRG
3omlA 206 gilpdilfne lkpkliapvv aylchesced ngsyiesaag watklhmvrg
TARGET h hhhhhh hhhhhhh hhh ssssss sssss
3omlA hhh hhhhhhh hhh ssssss sssss
TARGET 249 KGAVLRPSLD DPVTIEYVKD VWSNVTDMSK AKHLGAIAEA SGTLLEVLEK
3omlA 256 kgavlrpsld dpvtieyvkd vwsnvtdmsk akhlgaiaea sgtllevlek
TARGET hhhhh hhh hhh hhhhhhhhhh
3omlA hhhhh hhh hhh hhhhhhhhhh
TARGET 299 LKEGGGDAIE DAFEFNSKEL ITYALGIGAS VKNAKDMRFL YENDADFAAI
3omlA 306 lkegggdaie dafefnskel ityalgigas vknakdmrfl yendadfaai
TARGET hh ss sssss hhhh hhhhhh hhhhh
3omlA hh ss sssss hhhh hhhhhh hhhhh
TARGET 349 PTFFVLPGLL LQMSTDKLLS KALPNSQVDF SNILHGEQYL EIVDDLPTSG
3omlA 356 ptffvlpgll lqmstdk--- ---------- --ilhgeqyl eivddlptsg
TARGET h hhhhh hhh sssssss sss s
3omlA h hhhhh hhh sssssss sss s
TARGET 399 TLLTNGKVFD VMDKGSGAVV VTNSESFDES GRLLVRNQST TFIVGAGKFG
3omlA 406 tlltngkvfd vmdkgsgavv vtnsesfdes grllvrnqst tfivg-----
TARGET ssssssssss ssss ssss ssssssss sssssssss sss
3omlA ssssssssss ssss ssss ssssssss sssssssss sss
TARGET 449 GKKDPIAGVV PLQPAPNRQP DATVQYTTSE DQAALYRLSG DKNPLHIDPQ
3omlA 459 ---dpiagvv plqpapnrqp datvqyttse dqaalyrlsg dknplhidpq
TARGET ssssssss hhhhhhh hh
3omlA ssssssss hhhhhhhh hh
TARGET 499 MALLAGFKTP ILHGLCTLGF SVRAVLAQFA DNNPALFKAV KVRFSGPVIP
3omlA 506 mallagfktp ilhglctlgf svravlaqfa dnnpalfkav kvrfsgpvip
TARGET hhhhh hhhhhhh hhhhhhhh sssss sssss
3omlA hhhhh hhhhhhh hhhhhhhh sssss sssss
TARGET 549 GQTLRVDLWK QGTRINFRTV VVETGKEVIS GAYVDLK
3omlA 556 gqtlrvdlwk qgtrinfrtv vvetgkevis gayvdlk-
TARGET ssssssssss s ssssssss ss sssss ssssss
3omlA ssssssssss s ssssssss ss sssss ssssss
Template's ligands section
Template without ligands.
No ligands were included in the model.
Quaternary Structure Annotation of the Template
3oml 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: 3oml.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 (=DIMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.452 (>0.5 indicates similarity)
Template Selection
- Start SMR-Pipeline for:ea4f6c40f15968de3a65abc39625c1d1 on BC2-cluster at Fri Feb 22 03:30:41
2013
- Analyze BLAST summary ...
- Blast template search was successfull, number of templates selected for modeling: 1 go for
modeling ...
FATAL - No A3m found
- 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
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ******************************************************************************
- building model based on 3omlA (8-592) 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:ea4f6c40f15968de3a65abc39625c1d1 on BC2-cluster at Fri Feb 22 03:34:38
2013
Template Search
| Template Description |
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3oml: STRUCTURE OF FULL-LENGTH PEROXISOMAL MULTIFUNCTIONAL ENZYMFROM DROSOPHILA MELANOGASTER Solved by: X-RAY, Resolution: 2.15A, Identified by BLAST |
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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.