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 IDSVPT VAYKDQKPGT SGLRKKTKVF MDEPHYTENF IQATMQSIP-
1c47B 1 vk--ivtvkt kaypdqkpgt sglrkrvkvf qsstnyaenf iqsiistvep
TARGET sssss ssssshhh hh hhhhh hhhhhh
1c47B sssss ssssshhh hh hhhhh hhhhhh h
TARGET 46 NGSEGTTLVV GGDGRFYNDV IMNKIAAVGA ANGVRKLVIG QGGLLSTPAA
1c47B 49 aqrqeatlvv ggdgrfymke aiqlivriaa angigrlvig qngilstpav
TARGET sssss sss hhh hhhhhhhhhh hh ssssss s hhhh
1c47B hhh sssss s hhh hhhhhhhhhh h ssssss s hhhh
TARGET 96 SHIIRTYEEK CTGGGIILTA SHNPGGPEND LGIKYNLPNG GPAPESVTNA
1c47B 99 sciirkikai ---ggiilta shnpggpngd fgikfnisng gpapeaitdk
TARGET hhhhhh sssssss sss sss ssssssss sss hhhhhh
1c47B hhhhhh s ssssss sss sss ssssssss sss hhhhhh
TARGET 146 IWEASKKLTH YKIIKNFPKL NLNKLGKNQK YG-----PLL VDIIDPAKAY
1c47B 146 ifqisktiee yaicpdl-kv dlgvlgkqqf dlenkfkpft veivdsveay
TARGET hhhhh ss sss sssss ss ssss hhhh
1c47B hhhhhh ss sss sssss ss ssss hhhh
TARGET 191 VQFLKEIFDF DLIKSFLAKQ RKDKGWKLLF DSLNGITGPY GKAIFVDEFG
1c47B 195 atmlrnifdf nalkellsgp nr---lkiri damhgvvgpy vkkilceelg
TARGET hhhhhh h hhhhhhh ss s hhhh hhhhhhhhh
1c47B hhhhhh h hhhhhhh ss ss hhhh hhhhhhhhh
TARGET 241 LPAEEVLQNW HPLPDFGGLH PDPNLTYART LVDRVDREKI AFGAASDGDG
1c47B 242 apansav-nc vpledfgghh pdpnltyaad lvetmksgeh dfgaafdgdg
TARGET h hhhhhh ssssss
1c47B sss h hhhhhh sssss
TARGET 291 DRNMIYGYGP AFVSPGDSVA IIAEYAPEIP YFAKQGIYGL ARSFPTSSAI
1c47B 291 drnmilgkhg ffvnpsdsva viaanifsip yfqqtgvrgf arsmptsgal
TARGET sssss sss hhhhhh hhhh h hhhhh ss ssss hh
1c47B ssss sss hhhhhh hhhh h hhhhh ss ssss hh
TARGET 341 DRVAAKKGLR CYEVPTGWKF FCALFDAKKL SICGEESFGT GSNHIREKDG
1c47B 341 drvanatkia lyetptgwkf fgnlmdaskl slcgeesfgt gsdhirekdg
TARGET hhhhhhh s ssss hh hhhhhh sssss ss sss h
1c47B hhhhhhh s ssss hh hhhhhh sssss ss sss h
TARGET 391 LWAIIAWLNI LAIYHRRNPE KEASIKTIQD EFWNEYGRTF FTRYDYEHIE
1c47B 391 lwavlawlsi lat------- rkqsvedilk dhwhkfgrnf ftrydyeeve
TARGET hhhhhhhhhh hsss s ss hhhhhh hhhhhh sss ssssss ss
1c47B hhhhhhhhhh hhh h hhhhhh hhhhhh sss ssssss ss
TARGET 441 CEQAEKVVAL LSEFVSRPNV CGSHFPADES LTVIDCGD-F SYRD-LDGSI
1c47B 434 aegatkmmkd lealmfdrsf vgkqfsandk vytvekadnf eyhdpvdgsv
TARGET shhhhhhhhh hhhhh sss ssss
1c47B shhhhhhhhh hhhhh sss sssssssss ssss ss
TARGET 489 SENQGLFVKF SNGTKFVLRL SGTGSSGATI RLYVEKYTDK KENYGQTADV
1c47B 484 sknqglrlif adgsriifrl sgtgsagati rlyidsyekd nakinqdpqv
TARGET sssss s sssssss s sssss ssssssss hhh hhh
1c47B sss ssssss s sssssss s sssss ssssssss hhh hhh
TARGET 539 FLKPVINSIV KFLRFKEILG TDEPTVRT
1c47B 534 mlaplisial kvsqlqertg rtaptvit-
TARGET hhhhhhhhhh hh hhh sss
1c47B hhhhhhhhhh hh hhh sss
Template's ligands section
Ligands in the template:CD : 1.
Ligands in the template that will be assessed: CD562.
Model's ligands section
CD562
All the residues interacting with the ligand are completely conserved between model and template.
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.030
Given the properties calculated previously, the ligand B.CD562 will be included in the final model.
CD562: conservation:True, RMSD:True, included: True
The new model with the included ligands was saved successfully.
Quaternary Structure Annotation of the Template
1c47 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: 1c47.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 0.054 (>0.5 indicates similarity)
To build the complex the following chains of the complex has been additionally identified: 1c47A
Template Selection
- Start SMR-Pipeline for:d97795adbc187c81c315ef0187a030c0 on BC2-cluster at Mon Feb 18 18:28:06
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:
- 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 1c47B (5-570) 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:d97795adbc187c81c315ef0187a030c0 on BC2-cluster at Mon Feb 18 18:33:17
2013
Template Search
| Template Description |
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4hjh: IODIDE SAD PHASED CRYSTAL STRUCTURE OF A PHOSPHOGLUCOMUTASBRUCELLA MELITENSIS COMPLEXED WITH GLUCOSE-6-PHOSPHATE Solved by: X-RAY, Resolution: 2.10A, 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.