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Model Overview

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129

Sequence

UniProt

O15212

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

O15212: 9606.ENSP0000041

Domain

Link to: [ InterPro ]

Prefoldin_2

Model 3D Structure

	Model information:
	Modelled residue range:	1 to 113
	Based on template:	[ 2zqm ]
	Sequence Identity [%]:	20%
	Model date:	2012-10-27
	Revision date:	2012-10-15

Quaternary structure information:	[details]
Template (2zqm): TETRAMER Model built: SINGLE CHAIN

Ligand information:	[details]
Ligands in the template: GOL: 2. Ligands in the model: none.

Template Links: [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2012-10-15. 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 ]

Alignment


TARGET    1       MAELIQKK LQGEVEKYQQ LQKDLSKSMS GRQKLEAQLT ENNIVKEELA
2zqmA     1       mq-nippq vqamlgqles yqqqlqlvvq qkqkvqlelt eakkaldeie
                                                                      
TARGET                  hh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh
2zqmA                   hh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    49    LLDGSNVVFK LLGPVLVKQE LGEARATVGK RLDYITAEIK RYESQLRDLE
2zqmA     48    slpddavvyk tvgtlivktt kdkavaelke kietlevrln alerqekkln
                                                                      
TARGET                 sss ss  sssss  hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh
2zqmA                  sss ss  sssss  hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh


TARGET    99    RQSEQQRETL AQLQQ -                                    
2zqmA     98    eklkeltaqi qsalrpp                                    
                                                                      
TARGET          hhhhhhhhhh hhhh                                       
2zqmA           hhhhhhhhhh hhhh

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

Template's ligands section 
Ligands in the template: 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.

Oligomer Modelling Log

Quaternary Structure Annotation of the Template 
 2zqm is annotated as TETRAMER 
 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: 2zqm.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 (=TETRAMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.066 (>0.5 indicates similarity)

Template Selection

 - Start SMR-Pipeline for:5674276c9ec8dc5a830e1b3eb4292c60 on BC2-cluster at Sat Oct 27 01:16:06
2012 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with C found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - Proof template(s) selection compared to previous Repository update
 - Selected template(s): no changes compared to previous version of the Repository:
 -  Template: 2zqmA (1-113) Sequence Identity: 20.354
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -  **********************************************************************
 - building model based on 2zqmA (1-113) 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:5674276c9ec8dc5a830e1b3eb4292c60 on BC2-cluster at Sat Oct 27 01:22:35
2012

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

2zqm: CRYSTAL STRUCTURE OF THE PREFOLDIN BETA SUBUNIT FROM THERMOCOCCUS STRAIN KS-1
Solved by: X-RAY, Resolution: 1.90A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	14-122	2zqmA	16%	>target -----EKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG------E--ARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAK >2zqmA MQNIPPQVQAMLGQLESYQQQLQLVVQQKQKVQLELTEAKKALDEI---ES-----LPDDAVVYKTVGTLIVKTTKDKAVAELKEKIETLEVRLNALERQEKKLNEKLKELTAQIQSALRPP [Model]
	1-113	2zqmA	20%	>target MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQ-- >2zqmA MQ-NIPPQVQAMLGQLESYQQQLQLVVQQKQKVQLELTEAKKALDEIESLPDDAVVYKTVGTLIVKTTKDKAVAELKEKIETLEVRLNALERQEKKLNEKLKELTAQIQSALRPP [Model]

1fxk: CRYSTAL STRUCTURE OF ARCHAEAL PREFOLDIN (GIMC).
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

8-112	1fxkA	20%	>target -KLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQ- >1fxkA QNVQHQLAQFQQLQQQAQAISVQKQTVEMQINETQKALEELSRAADDAEVYKSSGNILIRVAKDELTEELQEKLETLQLREKTIERQEERVMKKLQEMQVNIQEAMK [Model]
8-113	1fxkB	20%	>target KLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQ--- >1fxkB NVQHQLAQFQQLQQQAQAISVQKQTVEMQINETQKALEELSRAADDAEVYKSSGNILIRVAKDELTEELQEKLETLQLREKTIERQEERVMKKLQEMQVNIQEAMKGAG [Model]
9-123	1fxkC	12%	>target --LQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGS--NVVFKLLG---------------------PVLVKQELGEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKA >1fxkC AALAEIVAQLNIYQSQVELIQQQMEAVRATISELEILEKTLSDIQGKDGSETLVPVGAGSFIKAELKDTSEVIMSVGAGVAIKKNFEDAMESIKSQKNELESTLQK-------MGENLRAITDIMMKLSPQAEELLAAVA [Model]
16-123	1fxkB	11%	>target -YQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEAR---------ATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKA >1fxkB NVQHQLAQFQQLQQQAQAISVQKQTVEMQINETQKALEELS--R------AADD-AEVYKSSGNILIRVAKDELTEELQEKLETLQLREKTIERQEERVMKKLQEMQVNIQEAMKGAG [Model]
15-119	1fxkA	11%	>target -KYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEAR---------ATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQ- >1fxkA QNVQHQLAQFQQLQQQAQAISVQKQTVEMQINETQKALEELS--R------AADD-AEVYKSSGNILIRVAKDELTEELQEKLETLQLREKTIERQEERVMKKLQEMQVNIQEAMK [Model]
17-49	1fxkC	15%	>target ---QQLQKDLSKSMSGRQKLEAQLTENNIVKEELAL------------------------------------------------------------------------------------------------- >1fxkC AALAEIVAQLNIYQSQVELIQQQMEAVRATISELEILEKTLSDIQGKDGSETLVPVGAGSFIKAELKDTSEVIMSVGAGVAIKKNFEDAMESIKSQKNELESTLQKMGENLRAITDIMMKLSPQAEELLAAVA [Model]

2zdi: CRYSTAL STRUCTURE OF PREFOLDIN FROM PYROCOCCUS HORIKOSHII OT3
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

11-110	2zdiA	16%	>target GEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQ- >2zdiA AMLGQLDTYQQQLQLVIQQKQKVQADLNEAKKALEEIETLPDDAQIYKTVGTLIVKTTKEKAVQELKEKIETLEVRLNALNRQEQKINEKVKELTQKIQAA [Model]
6-110	2zdiB	16%	>target QKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQ- >2zdiB PPQVQAMLGQLDTYQQQLQLVIQQKQKVQADLNEAKKALEEIETLPDDAQIYKTVGTLIVKTTKEKAVQELKEKIETLEVRLNALNRQEQKINEKVKELTQKIQAA [Model]
1-118	2zdiC	20%	>target MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGS----NVVF--------------------KLLG-PVLVKQELGEARATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRA------ >2zdiC MAQN-NKELEKLAYEYQVLQAQAQILAQNLELLNLAKAEVQTVRETLENLKKIEEEKPEILVPIGAGSFLKGVIVDKNNAIVSVGSGYAVERSIDEAISFLEKRLKEYDEAIKKTQGALAELEKRIGEVARKAQEVQQKQSMTSFKVKK [Model]
15-118	2zdiB	16%	>target --KYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEA---------RATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRA >2zdiB PPQVQAMLGQLDTYQQQLQLVIQQKQKVQADLNEAKKALEEI---ET-----LPDD-AQIYKTVGTLIVKTTKEKAVQELKEKIETLEVRLNALNRQEQKINEKVKELTQKIQAA [Model]
19-118	2zdiA	16%	>target -LQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEAR---------ATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRA >2zdiA AMLGQLDTYQQQLQLVIQQKQKVQADLNEAKKALEEIE---T-----LPDD-AQIYKTVGTLIVKTTKEKAVQELKEKIETLEVRLNALNRQEQKINEKVKELTQKIQAA [Model]
14-125	2zdiC	11%	>target -----EKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLL---G-PVLVK--------QELGE---AR----------ATVGKRLDYITAEIKRYESQLRDLERQSEQQRETLAQLQQEFQRAQAAKAGA------ >2zdiC MAQNNKELEKLAYEYQVLQAQAQILAQNLELLNLAKAEVQTVRETLENLKKIEEEKPEILVPIGAGSFLKGVIVDKNNAIVSVGSGYAVERSIDEAISFLEKRLKEYDEAIKKTQGALAELEKRIGEVARKAQEVQQKQSMTSFKVKK [Model]

Downloads

download model.tgz

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.