SWISS-MODEL Repository

[ Repository Query ] [ Full Text Query ]

SWISS-MODEL Repository - Model Details

Model Overview

Click on the bars to get more details about individual Models or experimental structures

331

Sequence

UniProt

P53034

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

P53034: 7227.FBpp0073120

Domain

Link to: [ InterPro ]

	AAA
	Rep_fac_C

Model 3D Structure

	Model information:
	Modelled residue range:	15 to 324
	Based on template:	[ 1sxj ]
	Sequence Identity [%]:	57%
	Model date:	2013-02-21
	Revision date:	2013-01-30

Quaternary structure information:	[details]
Template (1sxj): HETERO OCTAMER Model built :SINGLE CHAIN

Ligand information:	[details]
Ligands in the template: ATG: 2, MG: 1. 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        HLPWIEK YRPVKFKEIV GNEDTVARLS VFATQGNAPN IIIAGPPGVG
1sxjB     7     l--qlpwvek yrpqvlsdiv gnketidrlq qiakdgnmph miisgmpgig
                                                                      
TARGET                hhhh               hhhhhhh hhhh     s sssss     
1sxjB                 hhhh               hhhhhhh hhhh     s sssss     


TARGET    48    KTTTIQCLAR ILLGDSYKEA VLELNASNER GIDVVRNKIK MFAQQKVTLP
1sxjB     55    kttsvhclah ellgrsyadg vlelnasddr gidvvrnqik hfaqkklhlp
                                                                      
TARGET          hhhhhhhhhh hh   hhhhh  sss        hhhh   hh hhhh      
1sxjB           hhhhhhhhhh h   hhhhhh  sss        hhh   hhh hhhh      


TARGET    98    RGRHKIVILD EADSMTEGAQ QALRRTMEIY SSTTRFALAC NTSEKIIEPI
1sxjB     105   pgkhkivild eadsmtagaq qalrrtmely snstrfafac nqsnkiiepl
                                                                      
TARGET              ssssss s     hhhh    hh   h    ssssssss        hhh
1sxjB               ssssss s     hhhh    hh   h    ssssssss        hhh


TARGET    148   QSRCAMLRFT KLSDAQVLAK LIEVAKWEKL NYTEDGLEAI VFTAQGDMRQ
1sxjB     155   qsqcailrys klsdedvlkr llqiikledv kytndgleai iftaegdmrq
                                                                      
TARGET          hh  sssss     hhhhhhh hhhhhhh       hhhhhhh hhh    hhh
1sxjB           hh  sssss     hhhhhhh hhhhhhh       hhhhhhh hhh    hhh


TARGET    198   GLNNLQSTAQ GFGDITAENV FKVCDEPHPK LLEEMIHHCA ANDIHKAYK-
1sxjB     205   ainnlqstva ghglvnadnv fkivdsphpl ivkkml---l asnledsiqi
                                                                      
TARGET          hhhhhhhhhh       hhhh hhhh    hh hhhhhh        hhhh   
1sxjB           hhhhhhhhhh       hhh    hh    hh hhhhhh        hhhhhhh


TARGET    247   ILAKLWKLGY SPEDIIANIF RVCKRI-NID EHLKLDFIRE IGITHMKIID
1sxjB     252   lrtdlwkkgy ssidivttsf rvtknlaqvk esvrlemike iglthmrile
                                                                      
TARGET           hhh        hhhhhhhhh hhhhh      hhhhhhhhhh hhhhhhhhh 
1sxjB           hhh         hhhhhhhhh hhhhh      hhhhhhhhhh hhhhhhhhh 


TARGET    296   GINSLLQLTA LLAKL ---- -                               
1sxjB     302   gvgtylqlas mlakihklnn k                               
                                                                      
TARGET               hhhhh hhhhh                                      
1sxjB                hhhhh hhhhhhhhh

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

Template's ligands section 
Ligands in the template: ATG: 2, MG: 1. 
Ligands in the template that will be assessed: MG812. 
Model's ligands section 
MG812 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand MG812 will not be included in the final model. 
MG812: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

Oligomer Modelling Log

Quaternary Structure Annotation of the Template
1sxj is annotated as HETERO OCTAMER
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: 1sxj.pdb1.gz

Quaternary Structure Modelling of the Target Protein
1sxj_1

Template Selection

 - Start SMR-Pipeline for:539ad9f990f4982aa061c4160327cc69 on BC2-cluster at Thu Feb 21 21:26:12
2013 


 - 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 F found
 - No template with J found
 - No template with A found
 - No template with E found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with A found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with F found
 - No template with J found
 - No template with A found
 - No template with E found
 - No template with F found
 - No template with J found
 - No template with A found
 - No template with E found
 - No template with A found
 - No template with G found
 - No template with H found
 - No template with F found
 - No template with F found
 - No template with J found
 - No template with P found
 - No template with A found
 - No template with E found
 - No template with O found
 - No template with K found
 - No template with Q found
 - No template with R found
 - No template with P found
 - No template with A found
 - No template with G found
 - No template with H found
 - No template with F found
 - No template with A found
 - No template with E found
 - No template with F found
 - No template with J found
 - No template with A found
 - No template with G found
 - No template with H found
 - No template with F found
 - No template with F found
 - No template with J found
 - No template with A found
 - No template with E found
 - No template with K found
 - No template with O found
 - No template with D found
 - No template with E 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

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -     ***************************************************************************
 - building model based on 1sxjB (15-324) 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:539ad9f990f4982aa061c4160327cc69 on BC2-cluster at Thu Feb 21 21:28:43
2013

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

4gp6: POLYNUCLEOTIDE KINASE
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	52-72	4gp6B	24%	>target -----------IIIAGPPGVGKTTTIQCLARI------------------------------------------------------------------------------------------------------------------------------------------ >4gp6B SMKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLVSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQLKKSIKGLQREGFRYVYILNSPEEVEEVVFERQ [Model]
	52-72	4gp6A	24%	>target -----------IIIAGPPGVGKTTTIQCLARI------------------------------------------------------------------------------------------------------------------------------------------- >4gp6A SMKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLVSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEIAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQLKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP [Model]

4gp7: POLYNUCLEOTIDE KINASE
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	52-72	4gp7B	24%	>target -----------IIIAGPPGVGKTTTIQCLARI------------------------------------------------------------------------------------------------------------------------------------------- >4gp7B SMKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLMSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEMAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQMKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP [Model]
	52-72	4gp7A	24%	>target -----------IIIAGPPGVGKTTTIQCLARI------------------------------------------------------------------------------------------------------------------------------------------- >4gp7A SMKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLMSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEMAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQMKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP [Model]

3b85: CRYSTAL STRUCTURE OF PREDICTED PHOSPHATE STARVATION-INDUCEATPASE PHOH2 FROM CORYNEBACTERIUM GLUTAMICUM
Solved by: X-RAY, Resolution: 2.35A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	23-152	3b85B	15%	>target --RPVKFKEIVGNEDTVARLSVFATQGNAPNIIIAGPPGVGKTTTIQCLARILLGDSYKEAVLELNA----SNERG----------IDVVRNK-----IKMFAQQK------VTLPRG---RHKIVILDEADSMTEGAQQALRRTMEIYSSTTRFALACN---------------------------------------- >3b85B VIRPKTLG----QKHYVDAI---D-TN--TIVFGLGPAGSGKTYLAMAKAVQALQSKQVSRIILTRPAVEAGEKLGFLPDPYLRPLHDALRDMVEPEVIPKLMEAGIVEVAPLAYMRGRTLNDAFVILDEAQNTTPAQMKMFLTRL---GFGSKMVVTGDSGLRLVRHILRGVDDVHFSELTSSDVVRHQLVGHIVDAYE [Model]
	23-153	3b85A	15%	>target --RPVKFKEIVGNEDTVARLSVFATQGNAPNIIIAGPPGVGKTTTIQCLARILLGDSYKEAVLELNAS----NERG-----------IDVVRN-----KIKMFAQQKV------TLPRG---RHKIVILDEADSMTEGAQQALRRTMEIYSSTTRFALACNT-------------------------------------- >3b85A VIRPKTLG----QKHYVDAI---D-TN--TIVFGLGPAGSGKTYLAMAKAVQALQSKQVSRIILTRPAVEAGEKLGFLPGDPYLRPLHDALRDMVEPEVIPKLMEAGIVEVAPLAYMRGRTLNDAFVILDEAQNTTPAQMKMFLTRL---GFGSKMVVTGDGLRLVRHILRGVDDVHFSELTSSDVVRHQLVGHIVDAYE [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.