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Model Overview

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948

Sequence

UniProt

Q9Z0E2

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

Q9Z0E2: 10090.ENSMUSP000

Domain

Link to: [ InterPro ]

	VWC
	VWC
	VWC
	CHRD
	CHRD
	CHRD
	CHRD

Model 3D Structure

	Model information:
	Modelled residue range:	696 to 762
	Based on template:	[ 1u5m ]
	Sequence Identity [%]:	29%
	Model date:	2012-10-28
	Revision date:	2012-10-15

Quaternary structure information:	[details]
Template (1u5m): MONOMER Model built: SINGLE CHAIN

Ligand information:	[details]
Ligands in the template: none. 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           RDPN TCFFEGQQRP HGARWAPNYD PLCSLCICQR RTVICDPVVC
1u5mA     1     yvef--qeag scvqdgqryn dkdvwkpe-- -pcricvcdt gtvlcddiic
                                                                      
TARGET                      sss  sss               sssssss   sssssss  
1u5mA                       sss  sss               sssssss   sssssss  


TARGET    45    PPPS-CPHPV QALDQCCPVC PEKQ ---                        
1u5mA     46    edvkdclspe ipfgeccpic padlaaaa                        
                                                                      
TARGET                                                                
1u5mA

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

Template's ligands section 
Template without ligands. 
No ligands were included in the model.

Oligomer Modelling Log

Quaternary Structure Annotation of the Template 
 1u5m is annotated as MONOMER 
 The template structure (1u5m) 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: 29.412) 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:3e936918ce15414e7fb1d77fb9bdfe2d on BC2-cluster at Sun Oct 28 15:21:49
2012 


 - 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: 
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Selected template(s): no changes compared to previous version of the Repository:
 -  Template: 1u5mA (696-762) Sequence Identity: 29.412
 -  Template: 1u5mA (777-848) Sequence Identity: 26.027
 -  Template: 1u5mA (47-131) Sequence Identity: 24.419
 -  Template: 1u5mA (863-934) Sequence Identity: 22.973
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                            ******
 - building model based on 1u5mA (696-762) was successful 
 -                                                                   ******
 - building model based on 1u5mA (777-848) was successful 
 -     *******
 - building model based on 1u5mA (47-131) was successful 
 -                                                                          ******
 - building model based on 1u5mA (863-934) 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:3e936918ce15414e7fb1d77fb9bdfe2d on BC2-cluster at Sun Oct 28 15:23:04
2012

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

1u5m: STRUCTURE OF A CHORDIN-LIKE CYSTEINE-RICH REPEAT (VWC MODULE) FROM COLLAGEN IIA
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

696-762	1u5mA	29%	>target ----RDPNTCFFEGQQRPHGARWAPNYDPLCSLCICQRRTVICDPVVCPPPS-CPHPVQALDQCCPVCPEKQ---- >1u5mA YVEFQEAGSCVQDGQRYNDKDVWKPE---PCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCPICPADLAAAA [Model]
863-934	1u5mA	23%	>target -----GPRGCRFAGQWFPENQSWHPSVPPFGEMSCITCRCGAGVPHCERDDCSPPLSCGSG--KESRCCSHCTAQRSSE- >1u5mA YVEFQEAGSCVQDGQRYNDKDVWKP-------EPCRICVCDTGTVLCDDIICEDVKDCLSPEIPFGECCPICPADLAAAA [Model]
777-848	1u5mA	26%	>target -------EGCYFDGDRSWRAAGTRWHPVVPPFGLIKCAVCTCKGATGEVHCEKVQCPRLA-CAQPVRANPTDCCKQCPVG----- >1u5mA YVEFQEAGSCVQDG--QRYNDKDVWKP-------EPCRICVCD--TGTVLCDDIICEDVKDCLSPEIP-FGECCPICPADLAAAA [Model]
47-131	1u5mA	24%	>target -----GAAGCSFGGKVYALDETWHPDLGEPFGVMRCVLCACEAPQWARRGRGPGRVSCKNIKPQCPTLA-CRQPRQLPGHCCQTCPQERSN-- >1u5mA YVEFQEAGSCVQDGQRYNDKDVWKPE--------PCRICVCDT----------GTVLCDDII--CEDVKDCLSPEIPFGECCPICPADLAAAA [Model]

3bk3: CRYSTAL STRUCTURE OF THE COMPLEX OF BMP-2 AND THE FIRST VOWILLEBRAND DOMAIN TYPE C OF CROSSVEINLESS-2
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

696-760	3bk3D	22%	>target ----RDPNTCFFEGQQRPHGARWAPNYDPLCSLCICQRRTVICDPVVCPPPS--CPHPVQALDQCCPVCPE >3bk3D WLITGTEASCENEGEVLH-IPNITDN---PCISCVCLNQKAECKQEKCAPLAEDCALVVKQTGACCEKCKG [Model]
696-760	3bk3C	22%	>target ----RDPNTCFFEGQQRPHGARWAPNYDPLCSLCICQRRTVICDPVVCPPPS--CPHPVQALDQCCPVCPE >3bk3C WLITGTEASCENEGEVLH-IPNITDN---PCISCVCLNQKAECKQEKCAPLAEDCALVVKQTGACCEKCKG [Model]
69-127	3bk3D	23%	>target ------------------GEPFGVMRCVLCACEAPQWARRGRGPGRVSCKNIKPQCPTLA--CRQPRQLPGHCCQTCPQ >3bk3D WLITGTEASCENEGEVLHIPNITDNPCISCVCLN----------QKAECKQEK--CAPLAEDCALVVKQTGACCEKCKG [Model]
69-127	3bk3C	23%	>target ------------------GEPFGVMRCVLCACEAPQWARRGRGPGRVSCKNIKPQCPTLA--CRQPRQLPGHCCQTCPQ >3bk3C WLITGTEASCENEGEVLHIPNITDNPCISCVCLN----------QKAECKQEK--CAPLAEDCALVVKQTGACCEKCKG [Model]
776-846	3bk3D	21%	>target ------GEGCYFDGDRSWRAAGTRWHPVVPPFGLIKCAVCTCKGATGEVHCEKVQCPRLA--CAQPVRANPTDCCKQCP- >3bk3D WLITGTEASCENEGEV-LH--IPNI-------TDNPCISCVCL--NQKAECKQEKCAPLAEDCALVVKQ-TGACCEKCKG [Model]
776-846	3bk3C	21%	>target ------GEGCYFDGDRSWRAAGTRWHPVVPPFGLIKCAVCTCKGATGEVHCEKVQCPRLA--CAQPVRANPTDCCKQCP- >3bk3C WLITGTEASCENEGEV-LH--IPNI-------TDNPCISCVCL--NQKAECKQEKCAPLAEDCALVVKQ-TGACCEKCKG [Model]
865-929	3bk3D	19%	>target -------RGCRFAGQWFPENQSWHPSVPPFGEMSCITCRCGAGVPHCERDDCSPPL-SCGSG--KESRCCSHCTA >3bk3D WLITGTEASCENEGEVLH-IPNIT-------DNPCISCVCLNQKAECKQEKCAPLAEDCALVVKQTGACCEKCKG [Model]
865-929	3bk3C	19%	>target -------RGCRFAGQWFPENQSWHPSVPPFGEMSCITCRCGAGVPHCERDDCSPPL-SCGSG--KESRCCSHCTA >3bk3C WLITGTEASCENEGEVLH-IPNIT-------DNPCISCVCLNQKAECKQEKCAPLAEDCALVVKQTGACCEKCKG [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.