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Model Overview

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4711

Sequence

UniProt

Q7TPH6

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain

Link to: [ InterPro ]

	RCC1
	Filamin
	PHR
	PHR
	RCC1_2
	zf-RING_2

Model 3D Structure

	Model information:
	Modelled residue range:	1189 to 1349
	Based on template:	[ 3gbw ]
	Sequence Identity [%]:	99%
	Model date:	2013-02-22
	Revision date:	2013-01-30

Quaternary structure information:	[details]
Template (3gbw): MONOMER Model: MONOMER

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 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 ]

Alignment


TARGET    1       SKEDYSVV NRFESHGGGW GYSAHSVEAI RFSADTDILL GGLGLFGGRG
3gbw_1#1  1227    sledysvv nrfeshgggw gysahsveai rfsadtdill gglglfggrg
                                                                      
TARGET                 sss sssssss           sss sssss  sss sssss     
3gbw_1#1               sss sssssss           sss sssss  sss sssss     


TARGET    49    EYTAKIKLFE LGPDGGDHET DGDLLAETDV LAYDCAAREK YAMMFDEPVL
3gbw_1#1  1275  eytakiklfe lgpdggdhet dgdllaetdv laydcaarek yaxxfdepvl
                                                                      
TARGET           sssssssss s            ssssss   sss        sssss   ss
3gbw_1#1         sssssssss s  hhhh      ssssss   sss        sssss   ss


TARGET    99    LQAGWWYVAW ARVSGPSSDC GSHGQASITT DDGVIFQFKS SKKSNNGTDV
3gbw_1#1  1325  lqagwwyvaw arvsgpssdc gshgqasitt ddgvifqfks skksnngtdv
                                                                      
TARGET          s    sssss ssss     s ssssssssss    ssssss            
3gbw_1#1        s    sssss ssss     s ssssssssss    ssssss            


TARGET    149   NAGQIPQLLY RLP                                        
3gbw_1#1  1375  nagqipqlly rlp-                                       
                                                                      
TARGET          sss  sssss s                                          
3gbw_1#1        sss  sssss s

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 
 3gbw is annotated as MONOMER 
 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: 3gbw.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The quaternary structure can be assumed to be identical 
 Model was succesfully built as MONOMER.

Template Selection

 - Start SMR-Pipeline for:d7cea4d4741000921721ef53c50f6756 on BC2-cluster at Fri Feb 22 20:21:01
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  2
 - But still uncovered regions of the target sequence detected, go for: 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 C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:6): model based on new templates
 - Send 6 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                     ***
 - building model based on 3gbwA (1189-1349) was successful 
 -                              ***
 - building model based on 3hwjB (1685-1844) was successful 
 -                *
 - building model based on 3mvdL (904-989) was successful 
 -                **
 - building model based on 3kciA (876-986) was successful 
 -         ***
 - building model based on 3kciA (496-677) was successful 
 -                                                                             *
 - building model based on 2y43A (4456-4534) 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:d7cea4d4741000921721ef53c50f6756 on BC2-cluster at Fri Feb 22 20:26:32
2013

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

3gbw: CRYSTAL STRUCTURE OF THE FIRST PHR DOMAIN OF THE MOUSE MYCBINDING PROTEIN 2 (MYCBP-2)
Solved by: X-RAY, Resolution: 1.32A, Identified by BLAST
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

1189-1349

3gbwA

99%

3hwj: CRYSTAL STRUCTURE OF THE SECOND PHR DOMAIN OF MOUSE MYC- BINDING PROTEIN 2 (MYCBP-2)
Solved by: X-RAY, Resolution: 2.25A, Identified by BLAST
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	1685-1844	3hwjA	92%	>target -NRFTKTSQGRSWNTGNGSPDAICFAVDKPGIVVVGFAVYGGGGIHEYELEVLVDDSEHAGDSTHSHRWTSLELVKGTYTTDDSPSDIAEIRLDKVVPLKENVKYAVRLSNYGSRTANGDGGMTTVQCPDGVTFTFSTCSLSSNGTNQTRGQIPQILYYRS >3hwjA LNRFTKTSQGRSWNTGNGSPDAICFAVDKPGIVVVGFAVYGGGGIHEYELEVLVD------------RWTSLELVKGTYTTDDSPSDIAEIRLDKVVPLKENVKYAVRLRNYGSRTANGDGGMTTVQCPDGVTFTFSTCSLSSNGTNQTRGQIPQILYYRS [Model]
	1685-1844	3hwjB	93%	>target NRFTKTSQGRSWNTGNGSPDAICFAVDKPGIVVVGFAVYGGGGIHEYELEVLVDDSEHAGDSTHSHRWTSLELVKGTYTTDDSPSDIAEIRLDKVVPLKENVKYAVRLSNYGSRTANGDGGMTTVQCPDGVTFTFSTCSLSSNGTNQTRGQIPQILYYRS >3hwjB NRFTKTSQGRSWNTGNGSPDAICFAVDKPGIVVVGFAVYGGGGIHEYELEVLVDDS----------RWTSLELVKGTYTTDDSPSDIAEIRLDKVVPLKENVKYAVRLRNYGSRTANGDGGMTTVQCPDGVTFTFSTCSLSSNGTNQTRGQIPQILYYRS [Model]

2y43: RAD18 UBIQUITIN LIGASE RING DOMAIN STRUCTURE
Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	4457-4534	2y43B	19%	>target --------------ADDMCMICFTEALSAAPAIQLDCSHVFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN------HIVLKDLLDPIKELYEDV-- >2y43B SRWPPGLAVMKTIDDLLRCGICFEY-F-NIAMIIPQCSHNYCSLCIRKFLSYKT----------QCPTCCVTVTEPDLKNNRILDELVKSLNFARNHLLQ [Model]
	4456-4534	2y43A	20%	>target ------------DADDMCMICFTEALSAAPAIQLDCSHVFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH------IVLKDLLDPIKELYEDV--- >2y43A RWPPGLAVMKTIDDLLRCGICFEYF--NIAMIIPQCSHNYCSLCIRKFLSYKT----------QCPTCCVTVTEPDLKNNRILDELVKSLNFARNHLLQF [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.