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 MNASEFRR RGKEMVDYMA NYMEGIEGRQ VYPDVEPGYL RPLIPAAAPQ
3rchA 1 mnasefrr rgkemvdyva nymegiegrq vypdvepgyl rplipaaapq
TARGET hhhhhh hhhhhhhhhh hhhh h hh
3rchA hhhhhh hhhhhhhhhh hhh h h hh
TARGET 49 EPDTFEDIIN DVEKIIMPGV THWHSPYFFA YFPTASSYPA MLADMLCGAI
3rchA 49 epdtfediin dvekiimpgv thwhspyffa yfptassypa mladmlcgai
TARGET hhhhhh hhhh sss hhh hhhhhhhhhh
3rchA hhhhhh hhhh hhh hhhhhhhhhh
TARGET 99 GCIGFSWAAS PACTELETVM MDWLGKMLEL PKAFLNEKAG EGGGVIQGSA
3rchA 99 gci------s pacteletvm mdwlgkmlel pkaflnekag egggviqgsa
TARGET hhhhhhhhh hhhhhhhh ssssss h
3rchA hhhhhhhhh hhhhhhhh ssssss h
TARGET 149 SEATLVALLA ARTKVIHRLQ AASPELTQAA IMEKLVAYSS DQAHSSVERA
3rchA 149 seatlvalla artkvihrlq aaspeltqaa imeklvayss dqahssvera
TARGET hhhhhhhhhh hhhhhhhhhh hh hhh hhhh ssss s hhhhh
3rchA hhhhhhhhhh hhhhhhhhhh hh hhh hhhh ssss s hhhhh
TARGET 199 GLIGGVKLKA IPSDGNFAMR ASALQEALER DKAAGLIPFF MVATLGTTTC
3rchA 199 gliggvklka ipsdgnfamr asalqealer dkaaglipff mvatlgtttc
TARGET hhhh ssss s hhhhhhhhhh hhhh ss sssssss
3rchA hhhh ssss s hhhhhhhhhh hhhh ss sssssss
TARGET 249 CSFDNLLEVG PICNKEDIWL HVDAAYAGSA FICPEFRHLL NGVEFADSFN
3rchA 249 csfdnllevg picnkediwl hvdaayagsa ficpefrhll ngvefadsfn
TARGET ssss hhhhh hhhhhh ss sssshhhhhh h hh ssss
3rchA ssss hhhhh hhhhhh ss sssshhhhh hhhhhhh ssss
TARGET 299 FNPHKWLLVN FDCSAMWVKK RTDLTGAFRL DPTYLKHSHQ DSGLITDYRH
3rchA 299 fnph-wllvn fdcsamwvkk rtdltgaf-- ---------- ----------
TARGET s sss ssssss hhhhh s ssssssss sssssss
3rchA s ssssss hhhhh
TARGET 349 WQIPLGRRFR SLKMWFVFRM YGVKGLQAYI RKHVQLSHEF ESLVRQDPRF
3rchA 355 ------rrfr slkmwfvfrm ygvkglqayi rkhvqlshef eslvrqdprf
TARGET ss hhhhhhhhhh hhhhhhh hhhhhhhhhh hhhhh ss
3rchA hhhhhhhhhh hhhhhhh hhhhhhhhhh hhhhh ss
TARGET 399 EICVEVILGL VCFRLKGSNK VNEALLQRIN SAKKIHLVPC HLRDKFVLRF
3rchA 399 eicvevilgl vcfrlkgsnk vneallqrin sakkihlvpc hlrdkfvlrf
TARGET sss ss ssssss h hhhhhhhhhh hh sss ss ssssss
3rchA sss ss ssssss h hhhhhhhhhh hh s ss ssssss
TARGET 449 AICSRTVESA HVQRAWEHIK ELAADVLRAE RE
3rchA 449 aicsrtvesa hvqrawehik elaadvlrae re-
TARGET ss h hhhhhhhhhh hhhhhhhhh
3rchA ss h hhhhhhhhhh hhhhhhhhh
Template's ligands section
Ligands in the template:ALA : 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
3rch 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: 3rch.pdb1.gz
Quaternary Structure Modelling of the Target Protein
Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure
Hence, the oligomeric structures of the target and the template can be assumed to be similar (=DIMER)
The corresponding reliability score is 0.706 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 3rchB
Unfortunately, we were not able to built the model as DIMER.
Thus, the model was built as single chain.
Template Selection
- Start SMR-Pipeline for:22479ab86acf99ff423606c7b93935cb on BC2-cluster at Mon Feb 18 08:11:09
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
- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ********************************************************************************
- Oligomeric modeling of 3rchA was not successful, fall back to monomeric modeling
- building model based on 3rchA (1-480) 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:22479ab86acf99ff423606c7b93935cb on BC2-cluster at Mon Feb 18 08:14:11
2013
Template Search
| Template Description |
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3rbl: CRYSTAL STRUCTURE OF HUMAN AROMATIC L-AMINO ACID DECARBOXYIN THE APO FORM Solved by: X-RAY, Resolution: 3.24A, Identified by BLAST |
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3rbf: CRYSTAL STRUCTURE OF HUMAN AROMATIC L-AMINO ACID DECARBOXYIN THE APO FORM Solved by: X-RAY, Resolution: 2.90A, Identified by BLAST |
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3rch: CRYSTAL STRUCTURE OF HUMAN AROMATIC L-AMINO ACID DECARBOXYIN THE OPEN CONFORMATION WITH LLP AND PLP BOUND TO CHAIN-B RESPECTIVELY Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST |
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1js6: CRYSTAL STRUCTURE OF DOPA DECARBOXYLASE Solved by: X-RAY, Resolution: 2.60A, Identified by BLAST |
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1js3: CRYSTAL STRUCTURE OF DOPA DECARBOXYLASE IN COMPLEX WITH THINHIBITOR CARBIDOPA Solved by: X-RAY, Resolution: 2.25A, 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.